bmc_jvenn.tex 17.8 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 50 51 52 53 54 55 56 57 58 59 60 61 62 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 %% 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 %\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 99 \title{jvenn: an interactive venn diagram viewer.}  Jerome Mariette committed Mar 03, 2014 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% 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[ addressref={aff1}, % id's of addresses, e.g. {aff1,aff2} corref={aff1}, % id of corresponding address, if any noteref={n1}, % id's of article notes, if any email={jane.e.doe@cambridge.co.uk} % email address ]{\inits{JE}\fnm{Jane E} \snm{Doe}} \author[ addressref={aff1,aff2}, email={john.RS.Smith@cambridge.co.uk} ]{\inits{JRS}\fnm{John RS} \snm{Smith}} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors' addresses here %% %% %% %% Repeat \address commands as much as %% %% required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \address[id=aff1]{% % unique id \orgname{Department of Zoology, Cambridge}, % university, etc \street{Waterloo Road}, % %\postcode{} % post or zip code \city{London}, % city \cny{UK} % country } \address[id=aff2]{% \orgname{Marine Ecology Department, Institute of Marine Sciences Kiel}, \street{D\"{u}sternbrooker Weg 20}, \postcode{24105} \city{Kiel}, \cny{Germany} } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% 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 180 \parttitle{Background} %if any  Jerome Mariette committed Mar 05, 2014 181   Jerome Mariette committed Mar 04, 2014 182   Jerome Mariette committed Mar 03, 2014 183 184 \parttitle{Results} %if any  Jerome Mariette committed Mar 07, 2014 185 186 187 ... Currently there is no software that provides such features.  Jerome Mariette committed Mar 03, 2014 188 \parttitle{Conclusions} %if any  Jerome Mariette committed Mar 07, 2014 189 conclusions ....  Jerome Mariette committed Mar 03, 2014 190   Jerome Mariette committed Mar 03, 2014 191 192 193 194 195 196 197 198 199 200 201 \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{keyword}  Jerome Mariette committed Mar 03, 2014 202 203 204 205 \kwd{venn} \kwd{edward} \kwd{diagram} \kwd{jquery}  Jerome Mariette committed Mar 03, 2014 206 \kwd{javascript}  Jerome Mariette committed Mar 03, 2014 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 \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 249 \section*{Background}  Jerome Mariette committed Mar 04, 2014 250   Jerome Mariette committed Mar 05, 2014 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 The massive amounts of data generated by biological projects makes the analysis of such projects more and more difficult. In such a context, it is important to provide researchers with effective visualization tools to explore and extract relevant knowledge from these data sets. Data analysis often leads to the production of biological identifiers (gene names, operational taxonomic unit, ...) for which it is interesting to know intersections between samples. One of the most popular visualization chart is the Venn diagrams \cite{Venn1880} wich allows to identify shared and unshared identifiers providing an insight on the similarities between the data sets. Several Venn diagram applications are availble. Some of them such as BioVenn \cite{Hulsen2008} or venny \cite{venny} provides their users a web application with text areas as inputs to enter identifiers. Where the first one outputs a three lists area-proportional diagram, the second one offers a four lists diagram without any respect of area proportions. Canvasxpress \cite{canvasxpress} and the Google Chart API \cite{googleAPI}, meanwhile, are javascript libraries including Venn diagram features that can easily be embedded in any WEB site. These libraries can only have as inputs numbers corresponding to each intersections and cannot perform any calculations to otain them. We intruduce jvenn a javascript library aiming to be part of rich WEB environments helping scientists to analyse their data, such does already existing tools as jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap \cite{DeuPons2014}. Jvenn handles up to 6 lists venn diagram, can display Edwards-Venn diagram  Jerome Mariette committed Mar 07, 2014 270 271 \cite{Edwards2004}, can easily be embeded within any web site, allows to provide inputs data in three different formats (list/number/list+number), allows to export the diagram to png and permits to overload the callback  Jerome Mariette committed Mar 05, 2014 272 273 function to control users interactions. jvenn has already been used in several scientific publications to display sets and their overlapping areas \cite{Bianchia2013, Aravindraja2013}.  Jerome Mariette committed Mar 03, 2014 274   Jerome Mariette committed Mar 03, 2014 275   Jerome Mariette committed Mar 05, 2014 276 \section*{Implementation}  Jerome Mariette committed Mar 04, 2014 277   Jerome Mariette committed Mar 07, 2014 278 279 280 281 282 283 jvenn is a javascript library written as a jQuery plugin \cite{jquery} and can be embeded within any WEB applications by referencing the javascript file from an HTML page. For researchers who want to produce a Venn diagram from their identifiers, jvenn is also available as a WEB application at http://bioinfo.genotoul.fr/index.php?id=116. A full documentation to insert the plugin within a WEB application is included in the software package that can be downloaded from https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.  Jerome Mariette committed Mar 05, 2014 284   Jerome Mariette committed Mar 05, 2014 285 \section*{Results and Discussion}  Jerome Mariette committed Mar 04, 2014 286   Jerome Mariette committed Mar 07, 2014 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 The jvenn output is a chart of two to six areas in which each area represents one of the identifiers set define as input. The numbers of each overlaps are displayed and are clickable by the user to access the identifiers list belonging to the intersection. In order to ease overlaps understanding, when the user is over an intersection number, jvenn overlights the pointed classes and blurs the other ones. The library provides an option to define the data inputs: \textit{series}. The library accepts three different input formats. In case the \textit{series} are a list of value, the plugin will compute itself the overlaps between lists. The \textit{series} can also define the number to display for each intersections or can be defined as a mix of the first two formats. The resulting display is created with the help of the javascript canvas object which allows to export the chart as a png file. This last feature can be disabled in order to hide the exporting button from the user by setting the \textit{exporting} option to \textit{false}. jvenn handles up to six classes, what leads to display sixty three overlap numbers. Displaying and interacting with such a chart can be bulky and difficult. In such a case, jvenn propose a switch button panel which allows to activate or disactivate classes. The selected overlap number is then displayed and can be clicked just like the other ones. jvenn also provides the Edwards-Venn display (Fig. 2) available by setting the \textit{displayType} option to \textit{edwards}. This display gives a different graphical representation of the classes which can be clearer whith a 6 classes diagram. The WEB application creator can also overload the callback function defining the click on an overlap number. This can be done by defining the \textit{fnClickCallback} parameter. The overloading function has access to the \textit{this.listnames} and \textit{this.list} variables allowing the developer to control the users interactions with the jvenn plugin. This feature can be disabled by setting the \textit{disableClick} option to \textit{true}. As example, we produced two venn diagrams representing six samples SRR068049, SRR06805, SRR068051, SRR068052, SRR068053 and SRR068054 corresponding to sets of Operational Taxonomic Units observed under different conditions. Fig. 1 shows intersections between five of them using the Venn diagram display. In Fig. 2, jvenn overlights the intersection between three samples of the six ones used to create the Edwards-Venn diagram.  Jerome Mariette committed Mar 03, 2014 314   Jerome Mariette committed Mar 03, 2014 315 316 \section*{Conclusions}  Jerome Mariette committed Mar 07, 2014 317 318 319 jvenn is an easy-to-use library aiming to generate Venn and Edwards-Venn diagrams from lists of identifiers or from computed numbers. Its implementation as a javascript library allows whoever who have WEB programming skills to embed it within its WEB application without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012},  Jerome Mariette committed Mar 10, 2014 320 RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente} WEB applications.  Jerome Mariette committed Mar 07, 2014 321   Jerome Mariette committed Mar 03, 2014 322 \section*{Availability and requirements}  Jerome Mariette committed Mar 03, 2014 323   Jerome Mariette committed Mar 07, 2014 324 325 326 327 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 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Backmatter begins here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{backmatter} \section*{Competing interests} The authors declare that they have no competing interests. \section*{Author's contributions} Text for this section \ldots \section*{Acknowledgements}  Jerome Mariette committed Mar 03, 2014 343 344 345 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 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% 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 363 \bibliography{bmc_jvenn} % Bibliography file (usually '*.bib' )  Jerome Mariette committed Mar 03, 2014 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385  % 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 05, 2014 386 387 388 389 390  \caption{\csentence{A five lists Venn diagram.} A Venn diagram displaying overlaps between five different biological samples. When the user click on a number, the function called is the one specified by the application developper. On the top-right, the exporting module allows the user to download its diagram as a png file.}  Jerome Mariette committed Mar 03, 2014 391 392 393  \end{figure} \begin{figure}[h!]  Jerome Mariette committed Mar 05, 2014 394 395 396 397 398  \caption{\csentence{A six lists Edwards-Venn diagram.} When the user is pointing a specific number, the lists involved in the intersection are overlighted and the other ones are blurred. In this example, the user pointed the intersection between the samples SRR068049, SRR068051 and SRR068052 which contains twelve different identifiers.}  Jerome Mariette committed Mar 03, 2014 399 400 401 402  \end{figure} \end{backmatter} \end{document}