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

Commit f739d4e3 authored by Jerome Mariette's avatar Jerome Mariette

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......@@ -94,7 +94,8 @@
and Philippe Bardou and Claire Hoede and Anis Djari and C\'{e}dric
Cabau and Christophe Klopp},
journal = {PLOS one},
note = {in press},
year = {2014},
URL = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096821},
title = {RNAbrowse: RNA-seq de novo assembly results browser}
}
......
......@@ -136,6 +136,10 @@
noteref={n1}, % id's of article notes, if any
email={Jerome.Mariette@toulouse.inra.fr}
]{\inits{JM}\fnm{J\'{e}r\^{o}me} \snm{Mariette}}
\author[
addressref={aff1},
email={Frederic.Escudie@toulouse.inra.fr}
]{\inits{FE}\fnm{Frederic} \snm{Escudie}}
\author[
addressref={aff1},
email={Christophe.Djemiel@toulouse.inra.fr}
......@@ -200,8 +204,8 @@
\begin{abstract} % abstract
\parttitle{Background} %if any
The amount of rich Web applications allowing scientists to store, share and
analyze data on-line is increasing. This enhances the need of embeddable
The amount of rich Web applications allowing scientists to store,
share and analyze data on-line is increasing. This enhances the need of embeddable
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.
......@@ -211,7 +215,7 @@ 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
allows to control and customize all user interactions.
allows to control and customize user interactions.
\parttitle{Conclusions} %if any
We introduce jvenn, an open source component for Web environments helping
......@@ -280,10 +284,10 @@ http://bioinfo.genotoul.fr/jvenn.
\section*{Background}
Biological projects are increasingly multiplexing samples to assess differences
Biological projects are increasingly producing 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 data sets. Data analysis often compare lists of biological
between data sets. Data analysis often leads to compare lists of biological
identifiers (gene names, operational taxonomic unit, ...).
List intersection results are commonly visualized using Venn diagrams
\cite{Venn1880} presenting shared and unshared identifier counts. They provide a
......@@ -298,7 +302,7 @@ is an R package including functions to draw classical diagrams from two to five
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 only a three circles area-proportional diagram, the second one
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
......@@ -311,7 +315,7 @@ data, in the same spirit as already existing tools such as jbrowse
\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 overload the callback function
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
......@@ -343,18 +347,20 @@ counts \textit{series}, the plug-in will only display the graphical result. The
display is based on a JavaScript canvas object allowing to export the chart as a
PNG file. The intersection table can also be downloaded as a CSV file.
It contains a header line with all diagram area labels and in column all 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.
The Web application developer can also overload the callback function defining
the click on an intersection count. This can be done by defining
the \textit{fnClickCallback} parameter. The overloading function has 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
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.
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.
This function give 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
setting the \textit{disableClick} option to \textit{true}. To customize the
diagram display, the developer can also settle the \textit{colors} option.(Fig. 1)
diagram display, the developer can also settle the \textit{colors} option.
\section*{Results and Discussion}
......@@ -366,32 +372,32 @@ 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
areas are often too small to display the figures.
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) by setting the \textit{displayType} option to \textit{edwards}. It
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
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
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
and display the corresponding intersection counts. For all the diagrams, when
the intersection count size exceeds the allowed space, the value is substituted
by a question mark. The real value pops-up on mouse over. This behavior can be
disabled by setting the \textit{shortNumber} option to \textit{false}. Last, to
show the lists taking part in an intersection, jvenn highlights the
corresponding areas on mouse over, fading the others out.
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.
Scientists are usually interested in extracting identifier lists from some of
the intersections, therefore, jvenn implements an one-click function which
retrieves the names of the corresponding samples and the identifiers.
retrieves the names of the corresponding samples and the identifiers. Seeking
an identifier can also be done using the plugin. The intersection with the
matching identifier is highlighted so the user can visualize the lists sharing
it.
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
allows users to check the list size homogeneity. 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. Setting the
\textit{displayStat} to true enables this feature.
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.
jvenn's performance depends on the client browser. Using the running version
(link below) on a standard Linux computer (1 cpu, 4GB of RAM), it displays a six lists diagram of
......@@ -431,7 +437,7 @@ http://bioinfo.genotoul.fr/jvenn/example.html.
The authors declare that they have no competing interests.
\section*{Author's contributions}
JM conceived and designed the project. JM, PB, and CD implemented the project.
JM conceived and designed the project. JM, PB, FE and CD implemented the project.
CK evaluated software capabilities, and provided feedback on implementation. JM
and CK wrote the manuscript. All authors read and approved the final manuscript.
......
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