Commit 4987a041 authored by Jerome Mariette's avatar Jerome Mariette
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fix some spelling

parent 0b8ef172
......@@ -201,20 +201,20 @@
\begin{abstract} % abstract
\parttitle{Background} %if any
The amount of rich WEB applications allowing scientists to store, share and analyze data online is increasing.
This enhances the need of embadable visualization tools. In a first approach, scientists often produce lists
of known identifiers corresponding to the different experimental conditions. The Venn diagram is one of the most
popular charts presenting list comparison results.
This enhances the need of embadable 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.
\parttitle{Results} %if any
jvenn is a javascript library providing lists processing and Venn diagram displaying functions. It is the only library
able to handle up to 6 input lists presenting results as classical or Edwards-Venn diagrams. It permits any developper
to embed Venn diagramm visualization features in a WEB page. jvenn is fully configurable and allows developpers to control
able to handle up to 6 input lists presenting results as classical or Edwards-Venn diagrams. Using it, developpers can
easily embed Venn diagramm visualization features in WEB pages. jvenn is fully configurable and allows to control
and customize all user interactions.
\parttitle{Conclusions} %if any
We introduce jvenn a javascript library aiming to be part of rich WEB environments helping scientists to analyse
their data. The library package, comming with a full documentation and some integration examples, is freely
available at https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
We introduce jvenn an open source component for WEB environments helping scientists to analyse their data. The
library package, comming with a full documentation and some integration examples, is freely available at
https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
\end{abstract}
......@@ -279,24 +279,24 @@ available at https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/inde
Biological projects are increasingly multiplexing samples to assess differences between conditions or individuals,
thus, it is important to provide researchers with effective visualization tools to explore and extract
relevant differences between these data sets. Data analysis often leads produces lists of biological identifiers
(gene names, operational taxonomic unit, ...). One simple analysis is the comparison of the intersections of these
lists. A commonly used visualization chart is the Venn diagrams \cite{Venn1880} wich allows to identify
shared and unshared identifiers providing an insight on the similarities between the lists.
relevant differences between these data sets. Data analysis often produces lists of biological identifiers
(gene names, operational taxonomic unit, ...) which are then compared. List intersection
results are commonly visualized using Venn diagrams \cite{Venn1880} presenting shared and unshared identifier
counts, providing an insight on the similarities between the lists.
Venn diagrams are often used to present results on WEB pages. Thus, several Venn diagram applications are
availble. 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
four lists diagram without area proportion respect. Canvasxpress \cite{canvasxpress} and the Google Chart
API \cite{googleAPI}, meanwhile, are javascript libraries including Venn diagram features which can easily
be embedded in any WEB site. These libraries can only produce figures given the intersection counts but
be embedded in any WEB page. These libraries generate the graphical output given the intersection counts but
cannot perform the calculations on the lists.
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 6 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/count lists), exports PNG files and permits
to overload the callback function in order to control users interactions. jvenn has already been used in several scientific
to overload the callback function in order to control users interactions. jvenn has already been cited in several scientific
publications \cite{Bianchia2013, Aravindraja2013}.
......@@ -345,16 +345,16 @@ six.
\section*{Conclusions}
jvenn is an easy-to-use library aiming to generate Venn and Edwards-Venn diagrams from lists of identifiers or from
computed interaction counts. Its implementation as a javascript library allows whoever has WEB programming skills to embed it
within its WEB application without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse
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
within a WEB page without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse
\cite{Mariette} and WallProtDB \cite{SanClemente} WEB applications.
\section*{Availability and requirements}
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.
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.
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......@@ -416,20 +416,21 @@ the system and for pointing out features worth developing.
\section*{Figures}
\begin{figure}[h!]
\caption{\csentence{A six lists classic Venn diagram.}
A Venn diagram displaying overlaps between six different biological samples. When
the user clicks on a number, the function the application developper specified is called.
On the top-right, the exporting module allows the user to download its diagram as a PNG
This Venn diagram displays overlaps between six different biological samples. When
the user clicks on a figure, it calls the developper 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
disactivate lists to access a specific intersection count. On the bottom, some statistic
charts showing the lists size repartition and the number of common and specific elements.}
disactivate 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
diagram.}
\end{figure}
\begin{figure}[h!]
\caption{\csentence{A six lists Edwards-Venn diagram.}
When the user mouse is over a specific figure, the lists involved in the intersection
are highlighted and the other ones are fade out. In this example, the user pointed the
intersection between the samples SRR068049, SRR068051 and SRR068052 containing eight
different identifiers.}
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.}
\end{figure}
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