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%% BioMed_Central_Tex_Template_v1.06
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%  bmc_article.tex            ver: 1.06 %
%                                       %

%%IMPORTANT: do not delete the first line of this template
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%%  LaTeX template for BioMed Central  %%
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%%          <8 June 2012>              %%
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%%% additional documentclass options:
%  [doublespacing]
%  [linenumbers]   - put the line numbers on margins

%%% loading packages, author definitions

%\documentclass[twocolumn]{bmcart}% uncomment this for twocolumn layout and comment line below
\documentclass{bmcart}

%%% Load packages
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\usepackage{listings}
\usepackage{color}
\definecolor{gray}{rgb}{0.5,0.5,0.5}
\lstset{
  language=Java,
  showstringspaces=false,
  columns=flexible,
  basicstyle={\scriptsize \ttfamily},
  numbers=none,
  stringstyle=\color{gray},
  breaklines=true,
  breakatwhitespace=true
}
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%\usepackage{amsthm,amsmath}
%\RequirePackage{natbib}
%\RequirePackage{hyperref}
\usepackage[utf8]{inputenc} %unicode support
%\usepackage[applemac]{inputenc} %applemac support if unicode package fails
%\usepackage[latin1]{inputenc} %UNIX support if unicode package fails


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                             %%
%%  If you wish to display your graphics for   %%
%%  your own use using includegraphic or       %%
%%  includegraphics, then comment out the      %%
%%  following two lines of code.               %%
%%  NB: These line *must* be included when     %%
%%  submitting to BMC.                         %%
%%  All figure files must be submitted as      %%
%%  separate graphics through the BMC          %%
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%%  submitted article.                         %%
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\def\includegraphic{}
\def\includegraphics{}



%%% Put your definitions there:
\startlocaldefs
\endlocaldefs


%%% Begin ...
\begin{document}

%%% Start of article front matter
\begin{frontmatter}

\begin{fmbox}
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\dochead{Software}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                          %%
%% Enter the title of your article here     %%
%%                                          %%
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\title{jvenn: an interactive Venn diagram viewer.}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% Comment or delete the keys which are     %%
%% not used. Repeat \author command as much %%
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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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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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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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\begin{artnotes}
%\note{Sample of title note}     % note to the article
\note[id=n1]{Equal contributor} % note, connected to author
\end{artnotes}

\end{fmbox}% comment this for two column layout

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%%                                          %%
%% The Abstract begins here                 %%
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%% Please refer to the Instructions for     %%
%% authors on http://www.biomedcentral.com  %%
%% and include the section headings         %%
%% accordingly for your article type.       %%
%%                                          %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{abstractbox}

\begin{abstract} % abstract
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\parttitle{Background} %if any
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The amount of rich Web applications allowing scientists to store, share and
analyze data on-line is increasing. This enhances the need of embeddable
visualization tools. Scientists often produce lists of known identifiers
corresponding to different experimental conditions. The Venn diagram is one of
the most popular chart types used to present list comparison results.
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\parttitle{Results} %if any
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jvenn is a JavaScript library providing lists processing and Venn diagram
displaying functions. It is able to handle up to six input lists presenting
results as classical or Edwards-Venn diagrams. Using it, developers can easily
embed dynamic Venn diagrams in Web pages. jvenn is fully configurable and
allows to control and customize all user interactions.
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\parttitle{Conclusions} %if any
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We introduce jvenn, an open source component for Web environments helping
scientists to analyze their data. The library package, which comes with full
documentation and an integration example, is freely available at
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http://bioinfo.genotoul.fr/jvenn.
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\end{abstract}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                          %%
%% The keywords begin here                  %%
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%% Put each keyword in separate \kwd{}.     %%
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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}

% MSC classifications codes, if any
%\begin{keyword}[class=AMS]
%\kwd[Primary ]{}
%\kwd{}
%\kwd[; secondary ]{}
%\end{keyword}

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

\end{frontmatter}

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%%                                          %%
%% The Main Body begins here                %%
%%                                          %%
%% Please refer to the instructions for     %%
%% authors on:                              %%
%% http://www.biomedcentral.com/info/authors%%
%% and include the section headings         %%
%% accordingly for your article type.       %%
%%                                          %%
%% See the Results and Discussion section   %%
%% for details on how to create sub-sections%%
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%% use \cite{...} to cite references        %%
%%  \cite{koon} and                         %%
%%  \cite{oreg,khar,zvai,xjon,schn,pond}    %%
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%%%%%%%%%%%%%%%%%%%%%%%%% start of article main body
% <put your article body there>

%%%%%%%%%%%%%%%%
%% Background %%
%%

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\section*{Background}
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Biological projects are increasingly multiplexing samples to assess differences
between conditions or individuals, thus, it is important to provide researchers
with effective visualization tools to explore and extract relevant differences
between these data sets. Data analysis often produces lists of biological
identifiers (gene names, operational taxonomic unit, ...) which are then
compared. List intersection results are commonly visualized using Venn diagrams
\cite{Venn1880} presenting shared and unshared identifier counts, providing an
insight on the similarities between the lists.

Venn diagrams are often used to present results in Web pages. Thus, several Venn
diagram applications are available. BioVenn \cite{Hulsen2008} or venny
\cite{venny} are Web applications with identifier input text areas. Where the
first one offers only a three circles area-proportional diagram, the second one 
offers a four lists diagram without area proportion respect. 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 page. These libraries generate graphical output given the
intersection counts but cannot perform calculations on the lists. 
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\cite{Bronwen2012}
\cite{RVennDiagram}

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We introduce jvenn, a JavaScript library helping scientists to present their
data, in the same spirit as already existing tools such as jbrowse
\cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap
\cite{DeuPons2014}. jvenn handles up to six input lists, can display classical
or Edwards-Venn \cite{Edwards2004} diagrams, can easily be embedded in a Web
page, allows three different data formats (lists, intersection counts and count
lists), exports PNG or CSV files and permits to overload the callback function
in order to control users interactions. jvenn has already been cited in two
scientific publications \cite{Bianchia2013, Aravindraja2013} and is embedded
within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB
\cite{SanClemente} Web applications.
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\section*{Implementation}
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jvenn is a JavaScript library written as a jQuery plug-in \cite{jquery}. It can
be embedded by referencing the JavaScript file in an HTML page. For researchers
who want to produce a Venn diagram from their identifier lists, jvenn is also
available as a Web application at http://bioinfo.genotoul.fr/jvenn/example.html.
The installation documentation is included in the software package which can be
downloaded from http://bioinfo.genotoul.fr/jvenn.
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The library provides an option to define the data inputs: \textit{series}. It
accepts three different input formats described in Table 1. In the case of list
or count lists \textit{series} it will first execute a function to compute the
overlaps between lists and then display the chart. In the case of intersection
counts \textit{series}, the plug-in will only display the graphical result. The
display is based on a JavaScript canvas object allowing to export the chart as a
PNG file. This feature can be disabled by setting the \textit{exporting} option
to \textit{false} hiding the exporting button.
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The Web application developer can also overload the callback function defining
the click on an intersection count. 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 user interactions. This feature can be disabled by
setting the \textit{disableClick} option to \textit{true}. To customize the
diagram display, the developer can also settle the \textit{colors} option.
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\section*{Results and Discussion}

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Venn diagrams are commonly used to display list intersections because they are
simple to read and understand. This is true up to four lists but scientists are
interested in using it with more. This type of diagrams are able to present up
to six lists in the classical representations. Reaching this number, the
presented diagrams are not proportional to the list counts and the intersection
areas are often too small to display the figures. 

To present in a user-friendly manner five or six list diagrams, jvenn implements
several functionalities. First, the display can be switched to Edwards-Venn
(Fig. 2) by setting the \textit{displayType} option to \textit{edwards}. It
gives a clearer graphical representation for six list diagrams. To enhance the
figure's readability on the classical six lists Venn graphic it was decided not
to present all the values and to link some areas to their figures using lines.
This still did not permit to show all figures, therefore a switch button panel
(Fig. 1) was added. This panel enables to switch on and off the different lists
and display the corresponding intersection counts. For all the diagrams, when
the intersection count size exceeds the allowed space, the value is substituted
by a question mark. The real value pops-up on mouse over. This behavior can be
disabled by setting the \textit{shortNumber} option to \textit{false}. Last, to
show the lists taking part in an intersection, jvenn highlights the
corresponding areas on mouse over the figure and fades the others out.

Scientists are usually interested in extracting identifier lists from some of
the intersections, therefore, jvenn implements an one-click function which
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retrieves the names of the corresponding samples and the identifiers.
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Having an overview of the list size and comparing multiple diagrams can be
difficult using a Venn diagram. Thus, jvenn provides two extra charts (Fig. 1) 
bellow the Venn. The first one represents the input lists size histogram. It
allows users to check the list size homogeneity. The second one displays the
number of elements located in intersections of a certain size. This feature can
be used to compare the compactness of multiple Venn diagrams. Setting the
\textit{displayStat} to true enables this feature.
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jvenn's performance depends on the client browser. Using the running version
(link below) on a standard Linux computer, it displays a six lists diagram of 
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10 000 identifiers in two seconds.
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As examples, 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 the six of them using the classical Venn diagram display.
In Fig. 2, jvenn highlights the intersection between three samples out of six
from an Edwards-Venn diagram.
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\section*{Conclusions}

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jvenn is an easy-to-use library which generates Venn and Edwards-Venn diagrams
from lists of identifiers or from computed intersection counts. Its
implementation as a library allows whoever has some JavaScript programming
skills to embed it in a Web page without any dependancies.
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\section*{Availability and requirements}
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jvenn is freely available under the GNU General Public License (GPL) and can be
downloaded with an example and the full documentation at
http://bioinfo.genotoul.fr/jvenn  website. A running version is accessible at
http://bioinfo.genotoul.fr/jvenn/example.html.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                          %%
%% Backmatter begins here                   %%
%%                                          %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\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                       %%
%%                                                         %%
%%  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.         %%
%%                                                         %%
%%                                                         %%
%%  Note that the displayed Bibliography will not          %%
%%  necessarily be rendered by Latex exactly as specified  %%
%%  in the online Instructions for Authors.                %%
%%                                                         %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% 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}
% \end{thebibliography}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                               %%
%% Figures                       %%
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%% NB: this is for captions and  %%
%% Titles. All graphics must be  %%
%% submitted separately and NOT  %%
%% included in the Tex document  %%
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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 six lists classic Venn diagram.}
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      This Venn diagram displays overlaps between six different biological
      samples. When the user clicks on a figure, it calls the developer defined
      function. The icon located on the top-right, allows users to download the
      diagram as a PNG file. On the bottom-right of the chart, a switch button
      panel allowing to activate or dis-activate lists to access a specific
      intersection count. The charts showing the lists size repartition and the
      number of common and specific elements are located underneath the
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      diagram.}
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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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      On mouse over a figure, the shape corresponding to the list involved in
      the intersection are highlighted and the other ones faded out. In
      this example, the user points the intersection between samples SRR068049,
      SRR068051 and SRR068052 which contains eight different items.}
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      \end{figure}

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                               %%
%% Tables                        %%
%%                               %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Use of \listoftables is discouraged.
%%
\section*{Tables}
\begin{table}[h!]
\caption{Available formats and example for the \textit{series} option.}
      \begin{tabular}{cccc}
        \hline
        format & example\\ \hline
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        lists & 
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\begin{lstlisting}
series: [{
	name: 'sample1',
	data: ["Otu1", "Otu2", "Otu3", "Otu4", "Otu5", "Otu6", "Otu7"]
}, {
	name: 'sample2',
	data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"]
}]
\end{lstlisting}\\ \hline
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        intersection counts & 
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\begin{lstlisting}
series: [{
	name: {A: 'sample 1', B: 'sample 2', C: 'sample 3'},
	data: {A: 340, B: 562, C: 620, AB: 639, AC: 456, BC: 915, ABC: 552}
}]
\end{lstlisting}\\ \hline
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        count lists  &
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\begin{lstlisting}
series: [{
	name: 'sample1',
	data: ["Otu1", "Otu2", "Otu3", "Otu4", "Otu5", "Otu6", "Otu7"],
	values: [5, 15, 250, 20, 23, 58, 89]
}, {
	name: 'sample2',
	data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"],
	values: [90, 300, 10, 2, 45, 9]
}]
\end{lstlisting}\\ \hline
      \end{tabular}
\end{table}

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\end{backmatter}
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\end{document}