Maintenance - Mise à jour mensuelle Lundi 1 Juin 2020 entre 7h00 et 9h00

Commit 3eda6964 authored by Jerome Mariette's avatar Jerome Mariette

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......@@ -214,7 +214,7 @@ user interactions.
\parttitle{Conclusions} %if any
We introduce jvenn, an open source component for Web environments helping scientists to analyse their data. The
library package, which comes with full documentation and an integration example, is freely available at
https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
http://bioinfo.genotoul.fr/jvenn.
\end{abstract}
......@@ -284,9 +284,6 @@ relevant differences between these data sets. Data analysis often produces lists
results are commonly visualized using Venn diagrams \cite{Venn1880} presenting shared and unshared identifier
counts, providing an insight on the similarities between the lists.
\cite{Bronwen2012}
\cite{RVennDiagram}
Venn diagrams are often used to present results in Web pages. Thus, several Venn diagram applications are
available. BioVenn \cite{Hulsen2008} or venny \cite{venny} are Web applications with identifier input text
areas. Where the first one offers only a three circles area-proportional diagram, the second one offers a
......@@ -294,13 +291,17 @@ four lists diagram without area proportion respect. Canvasxpress \cite{canvasxpr
API \cite{googleAPI}, meanwhile, are JavaScript libraries including Venn diagram features which can easily
be embedded in any Web page. These libraries generate graphical output given the intersection counts but
cannot perform calculations on the lists.
\cite{Bronwen2012}
\cite{RVennDiagram}
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 or Edwards-Venn \cite{Edwards2004} diagrams, can easily be
embeded in a Web page, allows three different data formats (lists, intersection counts and count lists), exports PNG files and permits
to overload the callback function in order to control users interactions. jvenn has already been cited in two scientific
publications \cite{Bianchia2013, Aravindraja2013}.
publications \cite{Bianchia2013, Aravindraja2013} and is embeded within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and
WallProtDB \cite{SanClemente} Web applications.
\section*{Implementation}
......@@ -308,7 +309,7 @@ publications \cite{Bianchia2013, Aravindraja2013}.
jvenn is a JavaScript library written as a jQuery plugin \cite{jquery}. It can be embeded by referencing the JavaScript file
in an HTML page. For researchers who want to produce a Venn diagram from their identifier lists, jvenn is also available as a
Web application at http://bioinfo.genotoul.fr/index.php?id=116. The installation documentation is included in the software package
which can be downloaded from https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
which can be downloaded from http://bioinfo.genotoul.fr/jvenn.
The library provides an option to define the data inputs: \textit{series}. It accepts three different input formats discribed in
Table 1. In the case of list or count lists \textit{series} it will first execute a function to compute the overlaps between lists and then
......@@ -325,7 +326,7 @@ To customize the diagram display, the developer can also settle the \textit{colo
\section*{Results and Discussion}
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 interested in using it with more. Nowadays, this type of diagrams are able to present up to six lists in the classical representations.
scientists are interested in using it with more. This type of diagrams are able to present up to six lists in the classical representations.
Reaching this number, the presented diagrams are not proportional to the list counts and the intersection areas are often too small to display the
figures.
......@@ -357,16 +358,14 @@ six from an Edwards-Venn diagram.
\section*{Conclusions}
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 JavaScript library allows whoever has some Web programming skills to embed it
in a Web page without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and
WallProtDB \cite{SanClemente} Web applications.
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 skills to embed it in a Web page without any
dependancies.
\section*{Availability and requirements}
jvenn is freely available under the GNU General Public License (GPL) and can be downloaded with an example and the full documentation
at https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil webcite. A running version is accessible at
http://bioinfo.genotoul.fr/index.php?id=116.
at http://bioinfo.genotoul.fr/jvenn webcite. A running version is accessible at http://bioinfo.genotoul.fr/index.php?id=116.
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......@@ -215,7 +215,7 @@
<div class="row-fluid">
<div class="span12">
<p> Click on a venn diagram figure to display the linked elements: </p>
<textarea id="names" style="width: 100%;" wrap="off" rows="10"></textarea>
<textarea readonly id="names" style="width: 100%;" wrap="off" rows="10"></textarea>
</div>
</div>
</div>
......
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