bmc_jvenn.tex 24.2 KB
 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 %\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}  Jerome Mariette committed May 06, 2014 104 \dochead{Software}  Jerome Mariette committed Mar 03, 2014 105 106 107 108 109 110 111  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the title of your article here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  Jerome Mariette committed May 05, 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  email={Jerome.Mariette@toulouse.inra.fr} ]{\inits{JM}\fnm{J\'{e}r\^{o}me} \snm{Mariette}}  Jerome Mariette committed May 22, 2014 139 140 141 \author[ addressref={aff1}, email={Frederic.Escudie@toulouse.inra.fr}  Jerome Mariette committed Jun 02, 2014 142 ]{\inits{FE}\fnm{Fr\'{e}d\'{e}ric} \snm{Escudi\'{e}}}  Jerome Mariette committed Mar 11, 2014 143 144 145 146 \author[ addressref={aff1}, email={Christophe.Djemiel@toulouse.inra.fr} ]{\inits{CD}\fnm{Christophe} \snm{Djemiel}}  Jerome Mariette committed Mar 03, 2014 147 148 \author[ addressref={aff1,aff2},  Jerome Mariette committed Mar 11, 2014 149 150  email={Christophe.Klopp@toulouse.inra.fr} ]{\inits{CK}\fnm{Christophe} \snm{Klopp}}  Jerome Mariette committed Mar 03, 2014 151 152 153 154 155 156 157 158 159 160 161  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors' addresses here %% %% %% %% Repeat \address commands as much as %% %% required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \address[id=aff1]{% % unique id  Jerome Mariette committed Mar 11, 2014 162 163 164 165 166  \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 167 168 } \address[id=aff2]{%  Jerome Mariette committed Mar 11, 2014 169 170 171 172 173  \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 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% 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 206 \parttitle{Background} %if any  Jerome Mariette committed Jun 11, 2014 207 208 209 Venn diagrams are commonly used to present list comparison results. When the number of input lists exceeds four the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its readability.  Jerome Mariette committed Mar 04, 2014 210   Jerome Mariette committed Mar 03, 2014 211 \parttitle{Results} %if any  Jerome Mariette committed Jun 11, 2014 212 213 214 215 jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. With it, developers can easily embed dynamic Venn diagrams in Web pages. jvenn allows to control and customize user interactions.  Jerome Mariette committed Mar 07, 2014 216   Jerome Mariette committed Mar 03, 2014 217 \parttitle{Conclusions} %if any  Jerome Mariette committed May 12, 2014 218 219 We introduce jvenn, an open source component for Web environments helping scientists to analyze their data. The library package, which comes with full  Jerome Mariette committed Jun 11, 2014 220 documentation and an example, is freely available at  Jerome Mariette committed May 06, 2014 221 http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Mar 20, 2014 222   Jerome Mariette committed Mar 03, 2014 223   Jerome Mariette committed Mar 03, 2014 224 225 226 227 228 229 230 231 232 233 234 \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{keyword}  Jerome Mariette committed Mar 11, 2014 235 236 237 \kwd{Venn} \kwd{Edward-Venn} \kwd{vizualisation}  Jerome Mariette committed Mar 03, 2014 238 \kwd{jquery}  Jerome Mariette committed May 05, 2014 239 \kwd{JavaScript}  Jerome Mariette committed Mar 03, 2014 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 \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 282 \section*{Background}  Jerome Mariette committed Mar 04, 2014 283   Jerome Mariette committed Jun 02, 2014 284 List comparison results are often presented as Venn diagrams \cite{Venn1880}. In  Jerome Mariette committed Jun 11, 2014 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 a Venn diagram each list is figured by a transparent shape. Shape overlaps contain the elements shared between lists or more often the corresponding counts. In proportional Venn diagrams the size of a shape depends on the number of elements of the corresponding list intersection. Venn diagram with up to four lists are easy to read and understand, but they become difficult to interpret with more lists. To solve this problem, the Edwards-Venn \cite{Edwards2004} representation introduces new shapes providing a clearer view (Fig. 2). Many Venn diagram software packages are already available. The first six lines of Table 1 present a subset of selected packages with their features including maximum number of input lists, input data formats, Venn diagram layouts, application types and output formats. The table gives insight on several aspects of Venn diagram production : \begin{itemize} \item All applications handle only one input format. Most of them use input lists and compute the intersection counts. In the case of Canvas, the user will have to find another tool to produce the count table. \item VENNTURE is the only application able to use six input lists. It implements Edwards layout. It runs under MS-Windows and produces static MS-PowerPoint files. \item None of the web-applications or JavaScript libraries implements dynamic features easing the visualization of the results such as on mouse-over highlighting. \item Only one application permits to extract the identifier list for a given intersection enabling further analysis. \item Presented Web-applications and JavaScript libraries can use a maximum of four input lists. \item Proportional Venn diagrams are very limited in the number of lists they can display : maximum three. Therefore programs designed to display high number of lists will implement non proportional diagrams. \end{itemize} Hereafter we introduce jvenn, a JavaScript library, developed as a jQuery plug-in \cite{jquery}, including many features easing diagram production and enhancing their readability. The library has already been used and cited in two scientific publications \cite{Bianchia2013, Aravindraja2013}. It is already embedded in different Web applications such as nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente}.  Jerome Mariette committed Mar 03, 2014 324   Jerome Mariette committed Mar 05, 2014 325 \section*{Implementation}  Jerome Mariette committed Mar 04, 2014 326   Jerome Mariette committed Jun 11, 2014 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 This section presents different features of jvenn including input formats, intersection algorithm, output format, complementary diagrams and customization. The library accepts three different input formats : lists, intersection counts and count lists. All are JSON objects. Examples are presented in Table 1. Lists'' contain for each input a label and an identifier table. Intersection counts'' contain a correspondence table between labels and letters [A..F] and a table linking the intersection names formed by the successions of letters and the counts. Count lists'' are organized as Lists'' in which identifiers are replaced by their unique occurrences and their counts. With Count lists'' the figures presented in the diagram correspond to the sums of counts of all identifiers shared between lists. This has been used in diversity studies to present OTU (Operational Taxonomic Unit) read counts. For lists'' and count lists'', jvenn computes the intersection counts and displays the chart. For intersection counts'', it only displays the graphic. jvenn intersection computing algorithm is based on venny \cite{venny}. The display is based on a JavaScript canvas object allowing PNG export. The intersection table can also be downloaded as a CSV file. It contains a header line with the diagram area labels and, in column, the identifiers of the elements contained in the area. This feature can be disabled by setting the \textit{exporting} option to \textit{false}. For more than three lists diagrams, jvenn presents a switch button panel to highlight intersections (Fig. 1). It also provides two extra charts (Fig. 1) located bellow the Venn. The first one represents the input lists size histogram. The second one displays the number of elements in intersections of a certain size. It includes, as well, search and intersection identifiers export functions. The Web application developer can define the diagram display by setting the \textit{displayType} option to \textit{edwards} or \textit{classic}. Setting the \textit{shortNumber} option to \textit{false} will disable the default behavior of the plug-in to substitute the intersection count by a question mark if this one overflows its area. Setting the \textit{fnClickCallback} callback function allows to overload the intersection count click action. This function gives access to the \textit{this.listnames} and \textit{this.list} variables. This feature can be disabled by setting the \textit{disableClick} option to \textit{true}. Diagram colors can be modified using the \textit{colors} option. To simply produce a Venn diagram from identifier lists, jvenn is  Jerome Mariette committed May 12, 2014 369 370 371 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.  Jerome Mariette committed Mar 07, 2014 372   Jerome Mariette committed Mar 27, 2014 373 374 \section*{Results and Discussion}  Jerome Mariette committed Jun 11, 2014 375 376 377 378 Because they are simple to read and understand, Venn diagrams are commonly used to display list intersections. This is true for up to four lists. This type of diagram is able to present up to six lists in its classical representation. But then, the intersection areas are often too small to display the figures.  Jerome Mariette committed May 12, 2014 379   Jerome Mariette committed Jun 11, 2014 380 To present, in a user-friendly manner, five or six list diagrams, jvenn implements  Jerome Mariette committed May 22, 2014 381 (Fig. 1) several functionalities. First, the display can be switched to Edwards-Venn  Jerome Mariette committed Jun 11, 2014 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 (Fig. 2) which 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 the switch button panel (Fig. 1) was added. It enables to switch on and off the different lists and display the corresponding intersection counts. For all diagrams, when the intersection count length exceeds the allowed space, the value is substituted by a question mark. The value pops-up on mouse over. Last, to show the lists taking part in an intersection, jvenn highlights the corresponding shapes on mouse over, fading the others out. The extra charts presented under the Venn diagram simplify verification and comparison of multiple diagrams. The list size graph allows users to check the homogeneity of the input list sizes. The intersection size graph can be used to compare the compactness of multiple Venn diagrams. Scientists are usually interested in extracting identifier lists for some intersections, therefore, jvenn implements an one-click function which retrieves the names of the corresponding sets and the identifiers. To find an identifier one can use the search box. The shapes containing the matching identifier are then highlighted.  Jerome Mariette committed Mar 27, 2014 403   Jerome Mariette committed May 12, 2014 404 jvenn's performance depends on the client browser. Using the running version  Jerome Mariette committed May 22, 2014 405 on a standard Linux computer (1 cpu, 4GB of RAM), it displays a six lists diagram of  Jerome Mariette committed Mar 27, 2014 406 10 000 identifiers in two seconds.  Jerome Mariette committed Mar 27, 2014 407   Jerome Mariette committed Mar 03, 2014 408 409 \section*{Conclusions}  Jerome Mariette committed Jun 11, 2014 410 411 412 413 jvenn allows whoever has some JavaScript programming skills to embed Venn diagrams in a Web page without dependency. It has been designed following the examples of jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap \cite{DeuPons2014}.  Jerome Mariette committed Mar 07, 2014 414   Jerome Mariette committed Mar 03, 2014 415 \section*{Availability and requirements}  Jerome Mariette committed Mar 03, 2014 416   Jerome Mariette committed May 12, 2014 417 418 419 420 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.  Jerome Mariette committed Mar 07, 2014 421   Jerome Mariette committed Mar 03, 2014 422 423 424 425 426 427 428 429 430 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Backmatter begins here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{backmatter} \section*{Competing interests}  Jerome Mariette committed Mar 11, 2014 431 The authors declare that they have no competing interests.  Jerome Mariette committed Mar 03, 2014 432 433  \section*{Author's contributions}  Jerome Mariette committed May 22, 2014 434 JM conceived and designed the project. JM, PB, FE and CD implemented the project.  Jerome Mariette committed May 12, 2014 435 436 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 437 438  \section*{Acknowledgements}  Jerome Mariette committed Mar 03, 2014 439 We would like to acknowledge all our users for providing us useful feedback on  Jerome Mariette committed May 23, 2014 440 441 the system and for pointing out features worth developing. We thank the reviewers for their insightful and constructive comments.  Jerome Mariette committed Mar 03, 2014 442   Jerome Mariette committed Mar 03, 2014 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% 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 460 \bibliography{bmc_jvenn} % Bibliography file (usually '*.bib' )  Jerome Mariette committed Mar 03, 2014 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482  % 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 483  \caption{\csentence{A six lists classic Venn diagram.}  Jerome Mariette committed May 12, 2014 484  This Venn diagram displays overlaps between six different biological  Jerome Mariette committed Jun 11, 2014 485 486 487 488 489  samples. The icon, located on the top-right, allows users to download the diagram as a PNG file. The middle-right switch button panel allows to activate or dis-activate lists to access a specific intersection count. Charts showing the list size and intersection size repartition located underneath the diagram.}  Jerome Mariette committed Mar 03, 2014 490 491 492  \end{figure} \begin{figure}[h!]  Jerome Mariette committed Mar 05, 2014 493  \caption{\csentence{A six lists Edwards-Venn diagram.}  Jerome Mariette committed Jun 11, 2014 494  On mouse over a figure, the shape corresponding to the lists involved in  Jerome Mariette committed May 12, 2014 495  the intersection are highlighted and the other ones faded out. In  Jerome Mariette committed Jun 11, 2014 496  this example, the user pointed the intersection between samples SRR068049,  Jerome Mariette committed May 12, 2014 497  SRR068051 and SRR068052 which contains eight different items.}  Jerome Mariette committed Mar 03, 2014 498 499  \end{figure}  Jerome Mariette committed Mar 20, 2014 500 501 502 503 504 505 506 507 508 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Tables %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Use of \listoftables is discouraged. %% \section*{Tables}  Jerome Mariette committed Jun 10, 2014 509 510  \begin{table}[h!]  Jerome Mariette committed Jun 11, 2014 511 \caption{Features of a subset of already available software packages, and jvenn.}  Jerome Mariette committed Jun 10, 2014 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535  \begin{tabular}{c|cccccc} Application & Maximum & Layouts & Application & Proportionality & Input data & Output\\ & number of & & type & & formats & formats \\ & input lists & & & & & \\ \hline VENNTURE \cite{Bronwen2012} & 6 & Edwards & Stand-alone & No & Lists & Powerpoint,\\ & & & & & & Excel, CSV \\ \hline VennDiagram \cite{RVennDiagram} & 5 & Classical & R package & No & Lists & R object, TIFF \\ \hline BioVenn \cite{Hulsen2008} & 3 & Classical & Web application & Yes & Lists & SVG, PNG \\ \hline venny \cite{venny} & 4 & Classical & Web application & No & Lists & PNG \\ \hline Canvasxpress \cite{canvasxpress} & 4 & Classical & JavaScript library & No & Intersection counts & JavaScript canvas \\ \hline Google & 3 & Classical & JavaScript library & Yes & Lists & PNG \\  Jerome Mariette committed Jun 11, 2014 536  Chart API \cite{googleAPI} & & & & & & \\ \hline \hline  Jerome Mariette committed Jun 10, 2014 537 538 539 540 541 542 543 544 545 546  jvenn & 6 & Classical & Web application & No & Lists, & Interactive \\ & & and Edwards & and JavaScript library & & intersection counts & diagram, \\ & & & & & and count lists & PNG, CSV \end{tabular} \end{table}  Jerome Mariette committed Mar 20, 2014 547 548 549 550 \begin{table}[h!] \caption{Available formats and example for the \textit{series} option.} \begin{tabular}{cccc} \hline  Jerome Mariette committed Jun 11, 2014 551 552  format & example\\ \hline lists &  Jerome Mariette committed Mar 20, 2014 553 554 555 556 557 558 559 560 561 \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 Jun 11, 2014 562  intersection counts &  Jerome Mariette committed Mar 20, 2014 563 564 \begin{lstlisting} series: [{  Jerome Mariette committed Jun 05, 2014 565 566  name: {A: 'sample 1', B: 'sample 2'}, data: {A: ["Otu3", "Otu4", "Otu6"], B: ["Otu8", "Otu9"], AB: ["Otu1",  Jerome Mariette committed Jun 11, 2014 567  "Otu2", "Otu5", "Otu7"]} }],  Jerome Mariette committed Jun 05, 2014 568  values: {A: 3, B: 2, AB: 4}  Jerome Mariette committed Mar 20, 2014 569 \end{lstlisting}\\ \hline  Jerome Mariette committed Jun 11, 2014 570  count lists &  Jerome Mariette committed Mar 20, 2014 571 572 573 574 575 576 577 578 579 580 581 582 583 584 \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 585 \end{backmatter}  Jerome Mariette committed Mar 24, 2014 586 \end{document}