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 Jerome Mariette committed Mar 03, 2014 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 %% BioMed_Central_Tex_Template_v1.06 %% % % bmc_article.tex ver: 1.06 % % % %%IMPORTANT: do not delete the first line of this template %%It must be present to enable the BMC Submission system to %%recognise this template!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% LaTeX template for BioMed Central %% %% journal article submissions %% %% %% %% <8 June 2012> %% %% %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% For instructions on how to fill out this Tex template %% %% document please refer to Readme.html and the instructions for %% %% authors page on the biomed central website %% %% http://www.biomedcentral.com/info/authors/ %% %% %% %% Please do not use \input{...} to include other tex files. %% %% Submit your LaTeX manuscript as one .tex document. %% %% %% %% All additional figures and files should be attached %% %% separately and not embedded in the \TeX\ document itself. %% %% %% %% BioMed Central currently use the MikTex distribution of %% %% TeX for Windows) of TeX and LaTeX. This is available from %% %% http://www.miktex.org %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% 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  Jerome Mariette committed Mar 20, 2014 50 51 52 53 54 55 56 57 58 59 60 61 62 \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 }  Jerome Mariette committed Mar 03, 2014 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 %\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 %% %% submission process, not included in the %% %% submitted article. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \def\includegraphic{} \def\includegraphics{} %%% Put your definitions there: \startlocaldefs \endlocaldefs %%% Begin ... \begin{document} %%% Start of article front matter \begin{frontmatter} \begin{fmbox} \dochead{Research} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the title of your article here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  Jerome Mariette committed Mar 04, 2014 112 \title{jvenn: an interactive venn diagram viewer.}  Jerome Mariette committed Mar 03, 2014 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors here %% %% %% %% Specify information, if available, %% %% in the form: %% %% ={,} %% %% = %% %% Comment or delete the keys which are %% %% not used. Repeat \author command as much %% %% as required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \author[  Jerome Mariette committed Mar 11, 2014 129 130 131 132 133 134  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},  Jerome Mariette committed Mar 03, 2014 135 136  corref={aff1}, % id of corresponding address, if any noteref={n1}, % id's of article notes, if any  Jerome Mariette committed Mar 11, 2014 137 138 139 140 141 142  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}}  Jerome Mariette committed Mar 03, 2014 143 144 \author[ addressref={aff1,aff2},  Jerome Mariette committed Mar 11, 2014 145 146  email={Christophe.Klopp@toulouse.inra.fr} ]{\inits{CK}\fnm{Christophe} \snm{Klopp}}  Jerome Mariette committed Mar 03, 2014 147 148 149 150 151 152 153 154 155 156 157  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors' addresses here %% %% %% %% Repeat \address commands as much as %% %% required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \address[id=aff1]{% % unique id  Jerome Mariette committed Mar 11, 2014 158 159 160 161 162  \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  Jerome Mariette committed Mar 03, 2014 163 164 } \address[id=aff2]{%  Jerome Mariette committed Mar 11, 2014 165 166 167 168 169  \orgname{Plate-forme SIGENAE / GenPhySE, INRA}, % university, etc \street{Borde Rouge}, % \postcode{31326} % post or zip code \city{Castanet-Tolosan}, % city \cny{France} % country  Jerome Mariette committed Mar 03, 2014 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter short notes here %% %% %% %% Short notes will be after addresses %% %% on first page. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Abstract begins here %% %% %% %% 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  Jerome Mariette committed Mar 03, 2014 202 \parttitle{Background} %if any  Jerome Mariette committed Mar 24, 2014 203 204 205 206 The amount of rich WEB applications allowing scientists to store, share and analyze data online is increasing. This enhances the need of embadable visualization tools. In a first approach, scientists often produce lists of known identifiers corresponding to the different experimental conditions. The Venn diagram is one of the most popular charts presenting list comparison results.  Jerome Mariette committed Mar 04, 2014 207   Jerome Mariette committed Mar 03, 2014 208 \parttitle{Results} %if any  Jerome Mariette committed Mar 24, 2014 209 210 211 212 jvenn is a javascript library providing lists processing and Venn diagram displaying functions. It is the only library able to handle up to 6 input lists presenting results as classical or Edwards-Venn diagrams. It permits any developper to embed Venn diagramm visualization features in a WEB page. jvenn is fully configurable and allows developpers to control and customize all user interactions.  Jerome Mariette committed Mar 07, 2014 213   Jerome Mariette committed Mar 03, 2014 214 \parttitle{Conclusions} %if any  Jerome Mariette committed Mar 11, 2014 215 We introduce jvenn a javascript library aiming to be part of rich WEB environments helping scientists to analyse  Jerome Mariette committed Mar 20, 2014 216 217 218 their data. The library package, comming with a full documentation and some integration examples, is freely available at https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.  Jerome Mariette committed Mar 03, 2014 219   Jerome Mariette committed Mar 03, 2014 220 221 222 223 224 225 226 227 228 229 230 \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{keyword}  Jerome Mariette committed Mar 11, 2014 231 232 233 \kwd{Venn} \kwd{Edward-Venn} \kwd{vizualisation}  Jerome Mariette committed Mar 03, 2014 234 \kwd{jquery}  Jerome Mariette committed Mar 03, 2014 235 \kwd{javascript}  Jerome Mariette committed Mar 03, 2014 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 \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} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% 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%% %% %% %% use \cite{...} to cite references %% %% \cite{koon} and %% %% \cite{oreg,khar,zvai,xjon,schn,pond} %% %% \nocite{smith,marg,hunn,advi,koha,mouse}%% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%% start of article main body % %%%%%%%%%%%%%%%% %% Background %% %%  Jerome Mariette committed Mar 03, 2014 278 \section*{Background}  Jerome Mariette committed Mar 04, 2014 279   Jerome Mariette committed Mar 20, 2014 280 281 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  Jerome Mariette committed Mar 24, 2014 282 283 284 relevant differences between these data sets. Data analysis often leads produces lists of biological identifiers (gene names, operational taxonomic unit, ...). One simple analysis is the comparison of the intersections of these lists. A commonly used visualization chart is the Venn diagrams \cite{Venn1880} wich allows to identify  Jerome Mariette committed Mar 20, 2014 285 shared and unshared identifiers providing an insight on the similarities between the lists.  Jerome Mariette committed Mar 05, 2014 286   Jerome Mariette committed Mar 24, 2014 287 288 289 290 291 292 293 Venn diagrams are often used to present results on WEB pages. Thus, several Venn diagram applications are availble. 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 site. These libraries can only produce figures given the intersection counts but cannot perform the calculations on the lists.  Jerome Mariette committed Mar 05, 2014 294   Jerome Mariette committed Mar 24, 2014 295 296 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}.  Jerome Mariette committed Mar 25, 2014 297 298 jvenn handles up to 6 input lists, can display classical or Edwards-Venn \cite{Edwards2004} diagrams, can easily be embeded in a WEB page, allows three different data formats (lists/intersection counts/count lists), exports PNG files and permits  Jerome Mariette committed Mar 24, 2014 299 300 to overload the callback function in order to control users interactions. jvenn has already been used in several scientific publications \cite{Bianchia2013, Aravindraja2013}.  Jerome Mariette committed Mar 03, 2014 301   Jerome Mariette committed Mar 03, 2014 302   Jerome Mariette committed Mar 05, 2014 303 \section*{Implementation}  Jerome Mariette committed Mar 04, 2014 304   Jerome Mariette committed Mar 24, 2014 305 306 307 308 jvenn is a javascript library written as a jQuery plugin \cite{jquery}. It can be embeded 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/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.  Jerome Mariette committed Mar 07, 2014 309   Jerome Mariette committed Mar 05, 2014 310   Jerome Mariette committed Mar 05, 2014 311 \section*{Results and Discussion}  Jerome Mariette committed Mar 04, 2014 312   Jerome Mariette committed Mar 24, 2014 313 314 315 316 317 318 319 jvenn outputs a chart build from two to six identifier lists. Overlap counts are displayed and are clickable enabling to access identifiers list of the intersection. In order to ease overlaps understanding, on mouse over, jvenn highlights the intersection count and the corresponding conditions while bluring the others. The library provides an option to define the data inputs: \textit{series}. It accepts three different input formats discribed 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 display the chart. In the case of intersection counts \textit{series}, the plugin will only display the graphical results. The resulting  Jerome Mariette committed Mar 25, 2014 320 display is based on the javascript canvas object allowing to export the chart as a PNG file. This last feature can be disabled in order  Jerome Mariette committed Mar 24, 2014 321 322 323 to hide the exporting button from the user by setting the \textit{exporting} option to \textit{false}. jvenn handles up to six lists, which leads to display sixty three overlap areas. Displaying and interacting with such a chart  Jerome Mariette committed Mar 25, 2014 324 325 326 327 328 329 can be bulky and difficult, therefore jvenn proposes a switch button panel allowing to activate or disactivate lists (Fig. 1). The selected overlap count is then displayed and can be clicked. Moreover for a high readability of the diagram, when the intersection counts size exceeds the allowed space, the value is substituted by a question mark. The real value is then poped-up when the user mouse is over. This behaviour can be disabled by setting the \textit{shortNumber} option to \textit{false}. jvenn also provides the Edwards-Venn display (Fig. 2) available by setting the \textit{displayType} option to \textit{edwards}. This display gives a different graphical representation of the lists which is clearer for 6 list diagrams. The WEB application developer can also overload the callback function defining the click on an overlap number.  Jerome Mariette committed Mar 24, 2014 330 331 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  Jerome Mariette committed Mar 25, 2014 332 333 334 335 336 337 338 \textit{disableClick} option to \textit{true}. To customize the diagram display, the developer can also settle the \textit{colors} option. Having an overview of the input data and comparing multiple diagrams can be difficult when using a Venn vizualisation. Thus, in order to ease this step, jvenn provides two extra charts bellow the Venn diagram (Fig. 1). The first graph represents the input lists size histogram. This one allows the user to check the homogeneity of its lists size. As example, In Fig. 1, both SRR068051 and SRR068053 lists have more identifiers than other ones. The second graph, displays the number of elements shared by one to six lists. This feature can be used to compare multiple Venn diagrams in order to asses the similarities between the input lists. Setting the \textit{displayStat} to true enables this feature.  Jerome Mariette committed Mar 07, 2014 339 340 341  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  Jerome Mariette committed Mar 25, 2014 342 between six of them using the Venn diagram display. In Fig. 2, jvenn overlights the intersection between three samples out of  Jerome Mariette committed Mar 24, 2014 343 six.  Jerome Mariette committed Mar 07, 2014 344   Jerome Mariette committed Mar 03, 2014 345   Jerome Mariette committed Mar 03, 2014 346 347 \section*{Conclusions}  Jerome Mariette committed Mar 07, 2014 348 jvenn is an easy-to-use library aiming to generate Venn and Edwards-Venn diagrams from lists of identifiers or from  Jerome Mariette committed Mar 24, 2014 349 computed interaction counts. Its implementation as a javascript library allows whoever has WEB programming skills to embed it  Jerome Mariette committed Mar 11, 2014 350 351 within its WEB application without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente} WEB applications.  Jerome Mariette committed Mar 07, 2014 352   Jerome Mariette committed Mar 03, 2014 353 \section*{Availability and requirements}  Jerome Mariette committed Mar 03, 2014 354   Jerome Mariette committed Mar 07, 2014 355 356 357 358 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.  Jerome Mariette committed Mar 03, 2014 359 360 361 362 363 364 365 366 367 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Backmatter begins here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{backmatter} \section*{Competing interests}  Jerome Mariette committed Mar 11, 2014 368 The authors declare that they have no competing interests.  Jerome Mariette committed Mar 03, 2014 369 370  \section*{Author's contributions}  Jerome Mariette committed Mar 11, 2014 371 372 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.  Jerome Mariette committed Mar 03, 2014 373 374  \section*{Acknowledgements}  Jerome Mariette committed Mar 03, 2014 375 376 377 We would like to acknowledge all our users for providing us useful feedback on the system and for pointing out features worth developing.  Jerome Mariette committed Mar 03, 2014 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% 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  Jerome Mariette committed Mar 05, 2014 395 \bibliography{bmc_jvenn} % Bibliography file (usually '*.bib' )  Jerome Mariette committed Mar 03, 2014 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417  % or include bibliography directly: % \begin{thebibliography} % \bibitem{b1} % \end{thebibliography} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Figures %% %% %% %% NB: this is for captions and %% %% Titles. All graphics must be %% %% submitted separately and NOT %% %% included in the Tex document %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% Do not use \listoffigures as most will included as separate files \section*{Figures} \begin{figure}[h!]  Jerome Mariette committed Mar 25, 2014 418 419  \caption{\csentence{A six lists classic Venn diagram.} A Venn diagram displaying overlaps between six different biological samples. When  Jerome Mariette committed Mar 11, 2014 420  the user clicks on a number, the function the application developper specified is called.  Jerome Mariette committed Mar 25, 2014 421  On the top-right, the exporting module allows the user to download its diagram as a PNG  Jerome Mariette committed Mar 25, 2014 422 423 424  file. On the bottom-right of the chart, a switch button panel allowing to activate or disactivate lists to access a specific intersection count. On the bottom, some statistic charts showing the lists size repartition and the number of common and specific elements.}  Jerome Mariette committed Mar 03, 2014 425 426 427  \end{figure} \begin{figure}[h!]  Jerome Mariette committed Mar 05, 2014 428  \caption{\csentence{A six lists Edwards-Venn diagram.}  Jerome Mariette committed Mar 11, 2014 429 430  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  Jerome Mariette committed Mar 25, 2014 431 432  intersection between the samples SRR068049, SRR068051 and SRR068052 containing eight different identifiers.}  Jerome Mariette committed Mar 03, 2014 433 434  \end{figure}  Jerome Mariette committed Mar 20, 2014 435 436 437 438 439 440 441 442 443 444 445 446 447 448 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% 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  Jerome Mariette committed Mar 24, 2014 449  lists &  Jerome Mariette committed Mar 20, 2014 450 451 452 453 454 455 456 457 458 \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  Jerome Mariette committed Mar 24, 2014 459  intersection counts &  Jerome Mariette committed Mar 20, 2014 460 461 462 463 464 465 \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  Jerome Mariette committed Mar 24, 2014 466  count lists &  Jerome Mariette committed Mar 20, 2014 467 468 469 470 471 472 473 474 475 476 477 478 479 480 \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}  Jerome Mariette committed Mar 03, 2014 481 \end{backmatter}  Jerome Mariette committed Mar 24, 2014 482 \end{document}