bmc_jvenn.tex 26 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 Jul 23, 2014 207 208 209 210 Venn diagrams are commonly used to present list comparison results. For example, biologists show differences between gene lists originating from different conditions this way. It is also a standard tool to display method comparison results in bioinformatics. When the number  Jerome Mariette committed Jun 11, 2014 211 212 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 213   Jerome Mariette committed Mar 03, 2014 214 \parttitle{Results} %if any  Jerome Mariette committed Jun 11, 2014 215 216 217 218 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 219   Jerome Mariette committed Mar 03, 2014 220 \parttitle{Conclusions} %if any  Jerome Mariette committed May 12, 2014 221 222 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 223 documentation and an example, is freely available at  Jerome Mariette committed May 06, 2014 224 http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Mar 20, 2014 225   Jerome Mariette committed Mar 03, 2014 226   Jerome Mariette committed Mar 03, 2014 227 228 229 230 231 232 233 234 235 236 237 \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{keyword}  Jerome Mariette committed Mar 11, 2014 238 239 240 \kwd{Venn} \kwd{Edward-Venn} \kwd{vizualisation}  Jerome Mariette committed Mar 03, 2014 241 \kwd{jquery}  Jerome Mariette committed May 05, 2014 242 \kwd{JavaScript}  Jerome Mariette committed Mar 03, 2014 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 \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 285 \section*{Background}  Jerome Mariette committed Mar 04, 2014 286   Jerome Mariette committed Jul 24, 2014 287 288 289 290 291 292 With the advent of high-throughput biology the number of compared samples, within an experiment, is increasing. The analysis step often leads to the production of a biological identifier list, such as gene names or operational taxonomic units, for each sample. A common visualization chart is the Venn diagrams \cite{Venn1880} which allows to spot shared and unshared identifiers providing an insight on the similarities between the lists.  Jerome Mariette committed Jul 23, 2014 293 294  In a Venn diagram each list is figured by a transparent shape. Shape overlaps  Jerome Mariette committed Jun 11, 2014 295 296 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  Jerome Mariette committed Jul 24, 2014 297 elements of the corresponding list intersection. Venn diagrams with up to four  Jerome Mariette committed Jun 11, 2014 298 299 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}  Jerome Mariette committed Jul 24, 2014 300 representation introduces new shapes providing a clearer view (Fig. 2).  Jerome Mariette committed Jun 11, 2014 301 302 303 304  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,  Jerome Mariette committed Jul 15, 2014 305 306 307 308 309 310 311 312 application types and output formats. The table gives insight on several aspects of Venn diagram production and highlights that no WEB applications handle up to six lists. VENNTURE \cite{Bronwen2012} is the only application able to produce such diagrams but this one only implements Edwards layout and only runs under MS-Windows to produce static MS-PowerPoint files. 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.  Jerome Mariette committed Jun 11, 2014 313 314 315 316 317 318 319  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 320   Jerome Mariette committed Jul 15, 2014 321   Jerome Mariette committed Mar 05, 2014 322 \section*{Implementation}  Jerome Mariette committed Mar 04, 2014 323   Jerome Mariette committed Jul 15, 2014 324 \subsection*{Inputs}  Jerome Mariette committed Jun 11, 2014 325   Jerome Mariette committed Jul 24, 2014 326 327 328 329 330 331 332 333 334 335 336 337 The library accepts three different input formats : Lists'', Intersection counts'' and Count lists''. 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.  Jerome Mariette committed Mar 07, 2014 338   Jerome Mariette committed Jul 15, 2014 339 \subsection*{Display features}  Jerome Mariette committed Mar 27, 2014 340   Jerome Mariette committed Jul 15, 2014 341 342 343 Venn diagrams are commonly used 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 344   Jerome Mariette committed Jun 11, 2014 345 To present, in a user-friendly manner, five or six list diagrams, jvenn implements  Jerome Mariette committed Jul 24, 2014 346 347 several functionalities (Fig. 1). First, the display can be switched to Edwards-Venn (Fig. 2) which gives a clearer graphical representation for six list diagrams. To  Jerome Mariette committed Jun 11, 2014 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 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.  Jerome Mariette committed Jul 15, 2014 363 For more than three lists diagrams, jvenn presents a switch button panel to  Jerome Mariette committed Jul 24, 2014 364 365 highlight intersections (Fig. 1). It also provides two extra charts (Fig. 1) located bellow the Venn. The first one represents the input lists size  Jerome Mariette committed Jul 15, 2014 366 367 368 369 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.  Jerome Mariette committed Jul 24, 2014 370 371 372 373 374 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 375   Jerome Mariette committed Jul 15, 2014 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 \subsection*{Outputs} 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 customized by the developper. \subsection*{Web application} To simply produce a Venn diagram from identifier lists, jvenn is available as a Web application at http://bioinfo.genotoul.fr/jvenn/example.html (Fig. 3). The installation documentation is included in the software package which can be downloaded from http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Jul 23, 2014 392 393 394 395 396 397 \subsection*{Performances} jvenn's performance depends on the client browser. Using the running version on a standard Linux computer (one cpu, 4GB of RAM), it displays a six lists diagram of 10 000 identifiers in two seconds.  Jerome Mariette committed Jul 15, 2014 398 399 400  \section*{Results}  Jerome Mariette committed Jul 23, 2014 401 M.A. Dillies and colleagues \cite{Dillies2012} have compared seven RNA-Seq data  Jerome Mariette committed Jul 24, 2014 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 normalization methods and given a set of best practices to help biologists in their data processing. In table two, they have shown the differences between methods pair-wise. The raw data table provided by the team contains 5,277 lines and eight columns. The columns correspond to the different methods presented in the 'Differential expression analysis' section of the article. The data in the table was thresholded ($p < 0.05$) to produce the method specific gene name lists. Six out of seven methods were selected for further processing ; Med was left out. The lists were uploaded to the jvenn application and a Venn diagram was produced. Using the layout selector the diagram was shown in Edwards Venn format, in which all figures are accessible. This view presents all the lists overlaps between methods. Considering Fig. 2, the higher values are located in central areas of the graph showing that the methods share large portions of gene lists. The list of 484 gene shared by DESeq, TMM, UQ and FQ has been extracted by clicking on the corresponding figure. Gene G002562 was sought using the search box. It was found to be part of the five genes shared by FQ and UQ. The jvenn statistics show that the different methods produce gene lists with very different sizes (minimum 417 - maximum 1,249) and the most of the genes are shared between methods : 1,069 genes out of 1,347 shared by at least four methods. The same analysis was performed with VENNTURE, the only tool enabling to generate a six list Edwards Venn diagram. First the software package was installed on a computer running under MS-Windows. The six gene lists were loaded in an MS-Excel spreadsheet. VENNTURE was run using the spreadsheet as input generating a static MS-PowerPoint file containing the diagram and a MS-Excel file with all the intersection contents. The names of 484 genes shared by DESeq, TMM, UQ and FQ were found in the intersection spreadsheet. The diagram did not allow to search for gene G002562. Once more it was found in the intersection spreadsheet.  Jerome Mariette committed Jul 17, 2014 431   Jerome Mariette committed Jul 24, 2014 432 \section*{Discussion}  Jerome Mariette committed Jul 17, 2014 433   Jerome Mariette committed Jul 24, 2014 434 435 436 437 jvenn enables to compare up to six lists and dynamically to update the diagram by modifying the list content. Compared to VENNTURE it does not need any installation and gives access to a dynamic diagram providing simple functions to extract gene lists and perform searches.  Jerome Mariette committed Jul 17, 2014 438   Jerome Mariette committed Jul 24, 2014 439 440 jvenns' statistical view gives a simple a quick overview of the sizes of the different lists and of the overlaps. This enables to compare different Venn diagrams.  Jerome Mariette committed Jul 15, 2014 441   Jerome Mariette committed Jul 24, 2014 442 jvenn diagrams  Jerome Mariette committed Mar 27, 2014 443   Jerome Mariette committed Jul 24, 2014 444 445 446 447 448 dynamic : list extraction, identifier search no statistical view Multiple layouts  Jerome Mariette committed Jul 15, 2014 449   Jerome Mariette committed Jul 23, 2014 450   Jerome Mariette committed Jul 15, 2014 451   Jerome Mariette committed Mar 03, 2014 452 453 \section*{Conclusions}  Jerome Mariette committed Jul 24, 2014 454 455 456 457 jvenn allows programers, with moderate JavaScript experiences 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 458   Jerome Mariette committed Mar 03, 2014 459 \section*{Availability and requirements}  Jerome Mariette committed Mar 03, 2014 460   Jerome Mariette committed May 12, 2014 461 462 463 464 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 465   Jerome Mariette committed Mar 03, 2014 466 467 468 469 470 471 472 473 474 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Backmatter begins here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{backmatter} \section*{Competing interests}  Jerome Mariette committed Mar 11, 2014 475 The authors declare that they have no competing interests.  Jerome Mariette committed Mar 03, 2014 476 477  \section*{Author's contributions}  Jerome Mariette committed May 22, 2014 478 JM conceived and designed the project. JM, PB, FE and CD implemented the project.  Jerome Mariette committed May 12, 2014 479 480 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 481 482  \section*{Acknowledgements}  Jerome Mariette committed Mar 03, 2014 483 We would like to acknowledge all our users for providing us useful feedback on  Jerome Mariette committed May 23, 2014 484 485 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 486   Jerome Mariette committed Mar 03, 2014 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% 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 504 \bibliography{bmc_jvenn} % Bibliography file (usually '*.bib' )  Jerome Mariette committed Mar 03, 2014 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526  % 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 527  \caption{\csentence{A six lists classic Venn diagram.}  Jerome Mariette committed May 12, 2014 528  This Venn diagram displays overlaps between six different biological  Jerome Mariette committed Jun 11, 2014 529 530 531 532 533  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 534 535 536  \end{figure} \begin{figure}[h!]  Jerome Mariette committed Mar 05, 2014 537  \caption{\csentence{A six lists Edwards-Venn diagram.}  Jerome Mariette committed Jun 11, 2014 538  On mouse over a figure, the shape corresponding to the lists involved in  Jerome Mariette committed May 12, 2014 539  the intersection are highlighted and the other ones faded out. In  Jerome Mariette committed Jun 11, 2014 540  this example, the user pointed the intersection between samples SRR068049,  Jerome Mariette committed May 12, 2014 541  SRR068051 and SRR068052 which contains eight different items.}  Jerome Mariette committed Mar 03, 2014 542 543  \end{figure}  Jerome Mariette committed Mar 20, 2014 544 545 546 547 548 549 550 551 552 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Tables %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Use of \listoftables is discouraged. %% \section*{Tables}  Jerome Mariette committed Jun 10, 2014 553 554  \begin{table}[h!]  Jerome Mariette committed Jun 11, 2014 555 \caption{Features of a subset of already available software packages, and jvenn.}  Jerome Mariette committed Jun 10, 2014 556 557 558 559 560 561 562  \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 &  Jerome Mariette committed Jun 11, 2014 563 564  Powerpoint\\ & & & & & & and Excel \\ \hline  Jerome Mariette committed Jun 10, 2014 565 566  VennDiagram \cite{RVennDiagram} & 5 & Classical & R package & No & Lists  Jerome Mariette committed Jun 11, 2014 567 568  & R object \\ & & & & & & and TIFF \\ \hline  Jerome Mariette committed Jun 10, 2014 569 570  BioVenn \cite{Hulsen2008} & 3 & Classical & Web application & Yes &  Jerome Mariette committed Jun 11, 2014 571  Lists & SVG and PNG \\ \hline  Jerome Mariette committed Jun 10, 2014 572 573 574 575 576  venny \cite{venny} & 4 & Classical & Web application & No & Lists & PNG \\ \hline Canvasxpress \cite{canvasxpress} & 4 & Classical & JavaScript library &  Jerome Mariette committed Jun 11, 2014 577 578  No & Intersection & JavaScript \\ & & & & & counts & canvas \\ \hline  Jerome Mariette committed Jun 10, 2014 579 580 581  Google & 3 & Classical & JavaScript library & Yes & Lists & PNG \\  Jerome Mariette committed Jun 11, 2014 582  Chart API \cite{googleAPI} & & & & & & \\ \hline \hline  Jerome Mariette committed Jun 10, 2014 583 584 585 586  jvenn & 6 & Classical & Web application & No & Lists, & Interactive \\  Jerome Mariette committed Jun 11, 2014 587 588  & & and Edwards & and JavaScript & & intersection & diagram, \\ & & & library & & counts and & PNG and CSV \\  Jerome Mariette committed Jul 24, 2014 589  & & & & & Count lists &  Jerome Mariette committed Jun 10, 2014 590 591 592 593  \end{tabular} \end{table}  Jerome Mariette committed Mar 20, 2014 594 595 596 597 \begin{table}[h!] \caption{Available formats and example for the \textit{series} option.} \begin{tabular}{cccc} \hline  Jerome Mariette committed Jul 24, 2014 598 599  Format & Example\\ \hline Lists &  Jerome Mariette committed Mar 20, 2014 600 601 602 603 604 605 606 607 608 \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 Jul 24, 2014 609  Intersection counts &  Jerome Mariette committed Mar 20, 2014 610 611 \begin{lstlisting} series: [{  Jerome Mariette committed Jun 05, 2014 612 613  name: {A: 'sample 1', B: 'sample 2'}, data: {A: ["Otu3", "Otu4", "Otu6"], B: ["Otu8", "Otu9"], AB: ["Otu1",  Jerome Mariette committed Jun 11, 2014 614  "Otu2", "Otu5", "Otu7"]} }],  Jerome Mariette committed Jun 05, 2014 615  values: {A: 3, B: 2, AB: 4}  Jerome Mariette committed Mar 20, 2014 616 \end{lstlisting}\\ \hline  Jerome Mariette committed Jul 24, 2014 617  Count lists &  Jerome Mariette committed Mar 20, 2014 618 619 620 621 622 623 624 625 626 627 628 629 630 631 \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 632 \end{backmatter}  Jerome Mariette committed Mar 24, 2014 633 \end{document}