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genotoul-bioinfo
jvenn
Commits
4987a041
Commit
4987a041
authored
Mar 27, 2014
by
Jerome Mariette
Browse files
fix some spelling
parent
0b8ef172
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BMC_jvenn/bmc_jvenn.tex
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4987a041
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@@ -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, s
cientists often produce lists
of known identifiers
corresponding to
the
different experimental conditions. The Venn diagram is one of the most
popular charts
present
ing
list comparison results.
This enhances the need of embadable visualization tools.
S
cientists 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,
developper
s can
easily
embed Venn diagramm visualization features in WEB page
s
. 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 a
n 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 compar
ison of the
intersection
s of these
lists. A
commonly
used
visualiz
ation chart is the
Venn diagrams
\cite
{
Venn1880
}
wich allows to
identif
y
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
the
n
compar
ed. List
intersection
results are
commonly visualiz
ed using
Venn diagrams
\cite
{
Venn1880
}
presenting shared and unshared
identif
ier
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
sit
e. These libraries
can only produce figures
given the intersection counts but
be embedded in any WEB
pag
e. 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
us
ed in several scientific
to overload the callback function in order to control users interactions. jvenn has already been
cit
ed 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 inter
a
ction 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
generate
s
Venn and Edwards-Venn diagrams from lists of identifiers or from
computed inter
se
ction 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) a
t
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) a
nd 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.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
...
...
@@ -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 display
ing
overlaps between six different biological samples. When
the user clicks on a
number, the function the application
developper
speci
fied
is called
.
On the top-right, the exporting module
allows
the
user to download
its
diagram as a PNG
This
Venn diagram display
s
overlaps between six different biological samples. When
the user clicks on a
figure, it calls the
developper
de
fi
n
ed
function
.
The icon located on the top-right,
allows user
s
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 list
s
involved in the intersection
are highlighted and the other ones
are
fade out. In this example, the user point
ed
the
intersection between
the
samples SRR068049, SRR068051 and SRR068052 contain
ing
eight
different i
dentifier
s.
}
On
mouse over a figure, the
shape corresponding to the
list involved in the intersection
are highlighted and the other ones fade
d
out. In this example, the user point
s
the
intersection between samples SRR068049, SRR068051 and SRR068052
which
contain
s
eight
different i
tem
s.
}
\end{figure}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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