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

Commit 61fd351e authored by Jerome Mariette's avatar Jerome Mariette

update the background section

parent 7c65858c
......@@ -284,42 +284,39 @@ http://bioinfo.genotoul.fr/jvenn.
\section*{Background}
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.
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
first one offers a three circles area-proportional diagram, the second one
outputs a non-proportional four lists diagram. Canvasxpress
\cite{canvasxpress} and Google Chart API \cite{googleAPI} are
List comparison results are often presented as Venn diagrams \cite{Venn1880}. In
a Venn diagram each list is figured by a transparent shape, differents shapes
ovelap when elements are shared between the lists. The intersection counts are
usually presented in the corresponding shapes overlap. In proportionnal Venn
diagram the size of a shape depends on the number of elements in the
corresponding list. Venn diagram with up to four lists are easy to read and
understand, but are difficult to interpret with more lists. To overcome this
issue, the Edwards-Venn \cite{Edwards2004} representation introduce new shapes
that provides a clearer view for diagrams having more than four lists (Fig. 2).
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. VENNTURE
\cite{Bronwen2012} is a stand-alone application able to generate Edwards-Venn
outputs 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 nowadays also often included in Web pages. BioVenn
\cite{Hulsen2008} and venny \cite{venny} are Web applications with identifier
input text areas. The first one offers a three circles area-proportional
diagram, the second one outputs a non-proportional four lists diagram.
Canvasxpress \cite{canvasxpress} and Google Chart API \cite{googleAPI} are
JavaScript libraries including Venn diagram features which can easily be
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.
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 diagrams, can easily be embedded in a Web
page, allows three different data formats (lists, intersection counts and count
lists), exports PNG or CSV files and permits to redefine the callback function
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.
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.
Hereafter 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}. The library 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.
\section*{Implementation}
......
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