bmc_jvenn.tex 24.3 KB
Newer Older
Jerome Mariette's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
104
\dochead{Software}
Jerome Mariette's avatar
Jerome Mariette committed
105
106
107
108
109
110
111

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                          %%
%% Enter the title of your article here     %%
%%                                          %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

112
\title{jvenn: an interactive Venn diagram viewer.}
Jerome Mariette's avatar
Jerome Mariette committed
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:                             %%
%%   <key>={<id1>,<id2>}                    %%
%%   <key>=                                 %%
%% Comment or delete the keys which are     %%
%% not used. Repeat \author command as much %%
%% as required.                             %%
%%                                          %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\author[
Jerome Mariette's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
135
136
   corref={aff1},                       % id of corresponding address, if any
   noteref={n1},                        % id's of article notes, if any
Jerome Mariette's avatar
Jerome Mariette committed
137
138
   email={Jerome.Mariette@toulouse.inra.fr}
]{\inits{JM}\fnm{J\'{e}r\^{o}me} \snm{Mariette}}
Jerome Mariette's avatar
Jerome Mariette committed
139
140
141
142
\author[
   addressref={aff1},
   email={Frederic.Escudie@toulouse.inra.fr}
]{\inits{FE}\fnm{Frederic} \snm{Escudie}}
Jerome Mariette's avatar
Jerome Mariette committed
143
144
145
146
\author[
   addressref={aff1},
   email={Christophe.Djemiel@toulouse.inra.fr}
]{\inits{CD}\fnm{Christophe} \snm{Djemiel}}
Jerome Mariette's avatar
Jerome Mariette committed
147
148
\author[
   addressref={aff1,aff2},
Jerome Mariette's avatar
Jerome Mariette committed
149
150
   email={Christophe.Klopp@toulouse.inra.fr}
]{\inits{CK}\fnm{Christophe} \snm{Klopp}}
Jerome Mariette's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
167
168
}
\address[id=aff2]{%
Jerome Mariette's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
206
\parttitle{Background} %if any
Jerome Mariette's avatar
Jerome Mariette committed
207
208
The amount of rich Web applications allowing scientists to store,
share and analyze data on-line is increasing. This enhances the need of embeddable
Jerome Mariette's avatar
Jerome Mariette committed
209
210
211
visualization tools. Scientists often produce lists of known identifiers
corresponding to different experimental conditions. The Venn diagram is one of
the most popular chart types used to present list comparison results.
Jerome Mariette's avatar
Jerome Mariette committed
212

Jerome Mariette's avatar
Jerome Mariette committed
213
\parttitle{Results} %if any
Jerome Mariette's avatar
Jerome Mariette committed
214
215
216
217
jvenn is a JavaScript library providing lists processing and Venn diagram
displaying functions. It is able to handle up to six input lists presenting
results as classical or Edwards-Venn diagrams. Using it, developers can easily
embed dynamic Venn diagrams in Web pages. jvenn is fully configurable and
Jerome Mariette's avatar
Jerome Mariette committed
218
allows to control and customize user interactions.
Jerome Mariette's avatar
text v1    
Jerome Mariette committed
219

Jerome Mariette's avatar
Jerome Mariette committed
220
\parttitle{Conclusions} %if any
Jerome Mariette's avatar
Jerome Mariette committed
221
222
223
We introduce jvenn, an open source component for Web environments helping
scientists to analyze their data. The library package, which comes with full
documentation and an integration example, is freely available at
Jerome Mariette's avatar
Jerome Mariette committed
224
http://bioinfo.genotoul.fr/jvenn.
Jerome Mariette's avatar
Jerome Mariette committed
225

Jerome Mariette's avatar
Jerome Mariette committed
226

Jerome Mariette's avatar
Jerome Mariette committed
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's avatar
Jerome Mariette committed
238
239
240
\kwd{Venn}
\kwd{Edward-Venn}
\kwd{vizualisation}
Jerome Mariette's avatar
Jerome Mariette committed
241
\kwd{jquery}
242
\kwd{JavaScript}
Jerome Mariette's avatar
Jerome Mariette committed
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
% <put your article body there>

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

Jerome Mariette's avatar
Jerome Mariette committed
285
\section*{Background}
Jerome Mariette's avatar
Jerome Mariette committed
286

Jerome Mariette's avatar
Jerome Mariette committed
287
288
289
290
291
292
293
294
Biological experiments are often based on sample or condition comparison.
Thus, it is important to provide researchers with effective visualization 
tools to explore and extract relevant differences between data sets. Data
analysis often leads to compare lists of biological identifiers (gene names, 
Operational Taxonomic Unit (OTU), ...). List intersection results are commonly 
visualized using Venn diagrams \cite{Venn1880} presenting shared and unshared 
identifier counts. They provide a simple way to extract similarities and
differences between the lists.
Jerome Mariette's avatar
Jerome Mariette committed
295
296
297
298
299
300
301
302
303
304

Many Venn diagram software packages are already available. They can be classified 
using their type : stand-alone, library, Web applications, JavaScript library and 
their diagram layout: classical or Edwards. Edwards-Venn \cite{Edwards2004} representation provides
a clearer view for diagrams having more than four lists (Fig. 2). VENNTURE \cite{Bronwen2012}
is a stand-alone application able to generate this layout for up to six lists. VennDiagram \cite{RVennDiagram}
is an R package including functions to draw classical diagrams from two to five lists. 

Venn diagrams are also often included in Web pages.  BioVenn \cite{Hulsen2008} and venny
\cite{venny} are Web applications with identifier input text areas. The
Jerome Mariette's avatar
Jerome Mariette committed
305
first one offers a three circles area-proportional diagram, the second one 
Jerome Mariette's avatar
Jerome Mariette committed
306
307
outputs a non-proportional four lists diagram. Canvasxpress
\cite{canvasxpress} and Google Chart API \cite{googleAPI} are
Jerome Mariette's avatar
Jerome Mariette committed
308
JavaScript libraries including Venn diagram features which can easily be
Jerome Mariette's avatar
Jerome Mariette committed
309
310
embedded in any Web page. They respectively produce diagrams with up to four and three lists.
Both generate graphical outputs given the intersection counts but cannot calculate them. 
Jerome Mariette's avatar
Jerome Mariette committed
311

Jerome Mariette's avatar
Jerome Mariette committed
312
313
314
315
We introduce jvenn, a JavaScript library helping scientists to present their
data, in the same spirit as already existing tools such as jbrowse
\cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap
\cite{DeuPons2014}. jvenn handles up to six input lists, can display classical
Jerome Mariette's avatar
Jerome Mariette committed
316
or Edwards-Venn diagrams, can easily be embedded in a Web
Jerome Mariette's avatar
Jerome Mariette committed
317
page, allows three different data formats (lists, intersection counts and count
Jerome Mariette's avatar
Jerome Mariette committed
318
lists), exports PNG or CSV files and permits to redefine the callback function
Jerome Mariette's avatar
Jerome Mariette committed
319
320
321
322
in order to control users interactions. jvenn has already been cited in two
scientific publications \cite{Bianchia2013, Aravindraja2013} and is embedded
within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB
\cite{SanClemente} Web applications.
Jerome Mariette's avatar
Jerome Mariette committed
323

Jerome Mariette's avatar
Jerome Mariette committed
324

Jerome Mariette's avatar
Jerome Mariette committed
325
\section*{Implementation}
Jerome Mariette's avatar
Jerome Mariette committed
326

Jerome Mariette's avatar
Jerome Mariette committed
327
328
329
330
jvenn is based on venny regarding the algorithm computing the lists intersections.
The algorithm has been wrapped in a jQuery plug-in \cite{jquery}, extended with 
new features presented hereunder and the ability to use up to six lists. 
It can be embedded in an HTML page referencing the JavaScript file. For researchers
Jerome Mariette's avatar
Jerome Mariette committed
331
332
333
334
who want to produce a Venn diagram from their identifier lists, jvenn is also
available as a Web application at http://bioinfo.genotoul.fr/jvenn/example.html.
The installation documentation is included in the software package which can be
downloaded from http://bioinfo.genotoul.fr/jvenn.
Jerome Mariette's avatar
text v1    
Jerome Mariette committed
335

Jerome Mariette's avatar
Jerome Mariette committed
336
The library provides an option to define the input type : \textit{series}. It
Jerome Mariette's avatar
Jerome Mariette committed
337
338
339
accepts three different formats : lists, intersection counts and count lists. 
All are JSON objects. ``Lists'' contain for each input label and an
identifiers table. ``Intersection counts'' contain a correspondence table 
Jerome Mariette's avatar
Jerome Mariette committed
340
341
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'' 
Jerome Mariette's avatar
Jerome Mariette committed
342
343
344
345
346
347
348
349
in which identifiers are replaced by their unique occurrence and their count.
Examples are presented in Table 1. Venn diagrams show intersections between a
collection of sets. However, in some cases it can be interested to display not
just the sets but also their counts. As example, an OTU represents a species or
a group of species given by a cluster leader of DNA sequences. Displaying such
data with the ``lists'' format leads to produce intersections of shared and
unshared OTUs between samples. However, using ``count lists'' allows to define
the amount of sequences constituting each OTUs. Thus, the produced diagram
Jerome Mariette's avatar
Jerome Mariette committed
350
351
352
353
354
355
356
357
358
represents the species abondance between samples. For ``lists'' and ``count
lists'' jvenn will first execute a function to compute the intersections and 
display the chart. For ``intersection counts'', the plug-in  only displays
graphic. The display is based on a JavaScript canvas object  allowing to export 
it as a PNG file. 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. These features  can be 
disabled by setting the \textit{exporting} option to \textit{false} hiding the
exporting button.
Jerome Mariette's avatar
Jerome Mariette committed
359
360
361
362
363
364
365

The Web application developer can also define the diagram display setting the
\textit{displayType} option to \textit{edwards} or \textit{classic}. Setting the
\textit{shortNumber} option to \textit{false} will disable the default behaviour
of the plugin to substitute the intersection count by a question mark if this
one overflow its area. The callback function defining the click on an
intersection count can be overloaded by defining the \textit{fnClickCallback} parameter. 
Jerome Mariette's avatar
Jerome Mariette committed
366
367
This function gives 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 
Jerome Mariette's avatar
Jerome Mariette committed
368
setting the \textit{disableClick} option to \textit{true}. To customize the
Jerome Mariette's avatar
Jerome Mariette committed
369
diagram display, the developer can also set the \textit{colors} option.
Jerome Mariette's avatar
Jerome Mariette committed
370
371
372
373


\section*{Results and Discussion}

Jerome Mariette's avatar
Jerome Mariette committed
374
375
Venn diagrams are commonly used to display list intersections because they are
simple to read and understand. This is true up to four lists but scientists are
Jerome Mariette's avatar
Jerome Mariette committed
376
interested in using it with more. This type of diagram is able to present up
Jerome Mariette's avatar
Jerome Mariette committed
377
378
to six lists in its classical representation. Reaching this number, the
diagram can not a priori be proportional to the list counts and the intersection
Jerome Mariette's avatar
Jerome Mariette committed
379
380
areas are often too small to display the figures. 

Jerome Mariette's avatar
Jerome Mariette committed
381
382
383
384
To present in a user-friendly manner five or six list diagrams, jvenn implements
(Fig. 1) several functionalities. First, the display can be switched to Edwards-Venn
(Fig. 2) what 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
Jerome Mariette's avatar
Jerome Mariette committed
385
386
387
to present all the values and to link some areas to their figures using lines.
This still did not permit to show all figures, therefore a switch button panel
(Fig. 1) was added. This panel enables to switch on and off the different lists
Jerome Mariette's avatar
Jerome Mariette committed
388
and display the corresponding intersection counts. For all diagrams, when
Jerome Mariette's avatar
Jerome Mariette committed
389
the intersection count size exceeds the allowed space, the value is substituted
Jerome Mariette's avatar
Jerome Mariette committed
390
391
392
by a question mark. The real value pops-up on mouse over. Last, to show the
lists taking part in an intersection, jvenn highlights the corresponding areas on mouse over, 
fading the others out.
Jerome Mariette's avatar
Jerome Mariette committed
393
394
395

Scientists are usually interested in extracting identifier lists from some of
the intersections, therefore, jvenn implements an one-click function which
Jerome Mariette's avatar
Jerome Mariette committed
396
397
retrieves the names of the corresponding samples and the identifiers. Seeking
an identifier can also be done using the plugin. The intersection with the
Jerome Mariette's avatar
Jerome Mariette committed
398
matching identifier is highlighted as well as the lists containing it.
Jerome Mariette's avatar
Jerome Mariette committed
399

Jerome Mariette's avatar
Jerome Mariette committed
400
401
402
Having an overview of the list size and comparing multiple diagrams can be
difficult using a Venn diagram. Thus, jvenn provides two extra charts (Fig. 1) 
bellow the Venn. The first one represents the input lists size histogram. It
Jerome Mariette's avatar
Jerome Mariette committed
403
404
405
allows users to check the homogeneity of the lists size. The second one
displays the number of elements located in intersections of a certain size. This feature can
be used to compare the compactness of multiple Venn diagrams.
Jerome Mariette's avatar
Jerome Mariette committed
406

Jerome Mariette's avatar
Jerome Mariette committed
407
jvenn's performance depends on the client browser. Using the running version
Jerome Mariette's avatar
Jerome Mariette committed
408
on a standard Linux computer (1 cpu, 4GB of RAM), it displays a six lists diagram of 
Jerome Mariette's avatar
Jerome Mariette committed
409
10 000 identifiers in two seconds.
Jerome Mariette's avatar
Jerome Mariette committed
410

Jerome Mariette's avatar
Jerome Mariette committed
411
412
413
As examples, we produced two Venn diagrams representing six samples SRR068049,
SRR06805, SRR068051, SRR068052, SRR068053 and SRR068054 corresponding to sets of
Operational Taxonomic Units observed under different conditions. Fig. 1 shows
Jerome Mariette's avatar
Jerome Mariette committed
414
intersections between all of them using the classical Venn diagram display.
Jerome Mariette's avatar
Jerome Mariette committed
415
416
In Fig. 2, jvenn highlights the intersection between three samples out of six
from an Edwards-Venn diagram.
Jerome Mariette's avatar
text v1    
Jerome Mariette committed
417

Jerome Mariette's avatar
Jerome Mariette committed
418

Jerome Mariette's avatar
Jerome Mariette committed
419
420
\section*{Conclusions}

Jerome Mariette's avatar
Jerome Mariette committed
421
422
423
jvenn is an easy-to-use library which generates Venn and Edwards-Venn diagrams
from lists of identifiers or from computed intersection counts. Its
implementation as a library allows whoever has some JavaScript programming
Jerome Mariette's avatar
Jerome Mariette committed
424
skills to embed it in a Web page without any dependencies.
Jerome Mariette's avatar
text v1    
Jerome Mariette committed
425

Jerome Mariette's avatar
Jerome Mariette committed
426
\section*{Availability and requirements}
Jerome Mariette's avatar
Jerome Mariette committed
427

Jerome Mariette's avatar
Jerome Mariette committed
428
429
430
431
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's avatar
text v1    
Jerome Mariette committed
432

Jerome Mariette's avatar
Jerome Mariette committed
433
434
435
436
437
438
439
440
441
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                                          %%
%% Backmatter begins here                   %%
%%                                          %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{backmatter}

\section*{Competing interests}
Jerome Mariette's avatar
Jerome Mariette committed
442
The authors declare that they have no competing interests.
Jerome Mariette's avatar
Jerome Mariette committed
443
444

\section*{Author's contributions}
Jerome Mariette's avatar
Jerome Mariette committed
445
JM conceived and designed the project. JM, PB, FE and CD implemented the project.
Jerome Mariette's avatar
Jerome Mariette committed
446
447
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's avatar
Jerome Mariette committed
448
449

\section*{Acknowledgements}
Jerome Mariette's avatar
Jerome Mariette committed
450
451
452
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's avatar
Jerome Mariette committed
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                  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's avatar
Jerome Mariette committed
470
\bibliography{bmc_jvenn}      % Bibliography file (usually '*.bib' )
Jerome Mariette's avatar
Jerome Mariette committed
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492

% 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's avatar
Jerome Mariette committed
493
  \caption{\csentence{A six lists classic Venn diagram.}
Jerome Mariette's avatar
Jerome Mariette committed
494
495
496
497
498
499
500
      This Venn diagram displays overlaps between six different biological
      samples. When the user clicks on a figure, it calls the developer defined
      function. The icon located on the top-right, allows users to download the
      diagram as a PNG file. On the bottom-right of the chart, a switch button
      panel allowing to activate or dis-activate lists to access a specific
      intersection count. The charts showing the lists size repartition and the
      number of common and specific elements are located underneath the
Jerome Mariette's avatar
Jerome Mariette committed
501
      diagram.}
Jerome Mariette's avatar
Jerome Mariette committed
502
503
504
      \end{figure}

\begin{figure}[h!]
Jerome Mariette's avatar
Jerome Mariette committed
505
  \caption{\csentence{A six lists Edwards-Venn diagram.}
Jerome Mariette's avatar
Jerome Mariette committed
506
507
508
509
      On mouse over a figure, the shape corresponding to the list involved in
      the intersection are highlighted and the other ones faded out. In
      this example, the user points the intersection between samples SRR068049,
      SRR068051 and SRR068052 which contains eight different items.}
Jerome Mariette's avatar
Jerome Mariette committed
510
511
      \end{figure}

Jerome Mariette's avatar
Jerome Mariette committed
512
513
514
515
516
517
518
519
520
521
522
523
524
525
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                               %%
%% 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's avatar
Jerome Mariette committed
526
        lists & 
Jerome Mariette's avatar
Jerome Mariette committed
527
528
529
530
531
532
533
534
535
\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's avatar
Jerome Mariette committed
536
        intersection counts & 
Jerome Mariette's avatar
Jerome Mariette committed
537
538
539
540
541
542
\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's avatar
Jerome Mariette committed
543
        count lists  &
Jerome Mariette's avatar
Jerome Mariette committed
544
545
546
547
548
549
550
551
552
553
554
555
556
557
\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's avatar
Jerome Mariette committed
558
\end{backmatter}
Jerome Mariette's avatar
Jerome Mariette committed
559
\end{document}