Commit cf3a1779 authored by Jerome Mariette's avatar Jerome Mariette
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a first correction of the paper

parent c7070290
......@@ -5,7 +5,7 @@
title = {Cogwheels of the Mind: The Story of Venn Diagrams.},
publisher = {Johns Hopkins University Press},
year = {2004},
author = {Edwards A.W.F.},
author = {Anthony William Fairbank Edwards},
address = {Baltimore}
}
......@@ -20,9 +20,9 @@
}
@ARTICLE{Bianchia2013,
author = {L. Bianchia and A. Gagliardia and G. Campanellab and C. Landia and
A. Capaldoc and A. Carleod and A. Arminia and V. De Leoe and P. Piombonif
and R. Focarellic and L. Binia},
author = {Laura Bianchia and Assunta Gagliardi and Giovanna Campanella and Claudia Landi and
Anna Capaldo and Anna Carleo and Alessandro Armini and Vincenzo De Leo and Paola Piomboni and
Riccardo Focarelli and Luca Bini},
title = {A methodological and functional proteomic approach of human follicular
fluid en route for oocyte quality evaluation.},
journal = {Journal of Proteomics},
......@@ -48,9 +48,18 @@
pages = {488}
}
@ARTICLE{Bronwen2012,
author = {Bronwen Martin and Wayne Chadwick and Tie Yi and Sung-Soo Park and Daoyuan Lu
and Bin Ni and Shekhar Gadkaree and Kathleen Farhang and Kevin G. Becker and Stuart Maudsley},
title = {VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple
Pharmacological Dataset Analysis },
journal = {PLoS ONE},
year = {2012}
}
@ARTICLE{Lopes2010,
author = {Christian T. Lopes and Max Franz and Farzana Kazi and Sylva L. Donaldson
and Quaid Morris and Gary D. Bader},
author = {Christian Lopes and Max Franz and Farzana Kazi and Sylva Donaldson
and Quaid Morris and Gary Bader},
title = {Cytoscape Web: an interactive web-based network browser.},
journal = {Bioinformatics},
year = {2010}
......@@ -67,7 +76,7 @@
}
@article{Westesson01032013,
author = {Westesson, Oscar and Skinner, Mitchell and Holmes, Ian},
author = {Westesson Oscar and Skinner Mitchell and Holmes Ian},
title = {Visualizing next-generation sequencing data with JBrowse},
volume = {14},
number = {2},
......@@ -90,7 +99,7 @@
}
@OTHER{SanClemente,
author = {H. San Clemente and E. Jamet},
author = {Helene San Clemente and Elisabeth Jamet},
journal = {Database},
note = {in press},
title = {WallProtDB, a database resource for plant cell wall proteomics}
......@@ -122,7 +131,15 @@
}
@OTHER{venny,
author = {Juan Oliveros},
title = {An interactive tool for comparing lists with Venn Diagrams.},
url = {http://bioinfogp.cnb.csic.es/tools/venny/index.html}
url = {http://bioinfogp.cnb.csic.es/tools/venny/index.html},
year = {2007}
}
@OTHER{RVennDiagram,
author = {Hanbo Chen},
year = {2013},
title = {VennDiagram: Generate high-resolution Venn and Euler plots.},
url = {http://cran.r-project.org/web/packages/VennDiagram/index.html}
}
......@@ -109,7 +109,7 @@
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\title{jvenn: an interactive venn diagram viewer.}
\title{jvenn: an interactive Venn diagram viewer.}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
......@@ -200,20 +200,20 @@
\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. Scientists often produce lists of known identifiers
The amount of rich Web applications allowing scientists to store, share and analyze data online 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.
\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. Using it, developpers can
easily embed dynamic Venn diagramms in WEB pages. jvenn is fully configurable and allows to control and customize all
jvenn is a JavaScript library providing lists processing and Venn diagram displaying functions. It is the only library
able to handle up to six input lists presenting results as classical or Edwards-Venn diagrams. Using it, developers can
easily embed dynamic Venn diagramms in Web pages. jvenn is fully configurable and allows to control and customize all
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, comming with a full documentation and an integration example, is freely available at
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.
......@@ -232,7 +232,7 @@ https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil
\kwd{Edward-Venn}
\kwd{vizualisation}
\kwd{jquery}
\kwd{javascript}
\kwd{JavaScript}
\end{keyword}
% MSC classifications codes, if any
......@@ -284,36 +284,39 @@ 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.
Venn diagrams are often used to present results in WEB pages. Thus, several Venn diagram applications are
availble. BioVenn \cite{Hulsen2008} or venny \cite{venny} are WEB applications with identifier input text
\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
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 page. These libraries generate the graphical output given the intersection counts but
cannot perform the calculations on the lists.
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.
We introduce jvenn, a javascript library helping scientists to present their data, in the same spirit as already
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
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}.
\section*{Implementation}
jvenn is a javascript library written as a jQuery plugin \cite{jquery}. It can be embeded by referencing the javascript file
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
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.
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
display the chart. In the case of intersection counts \textit{series}, the plugin will only display the graphical result. The display
is based on a javascript canvas object allowing to export the chart as a PNG file. This feature can be disabled by setting the \textit{exporting}
is based on a JavaScript canvas object allowing to export the chart as a PNG file. This feature 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 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 setting the \textit{disableClick} option to \textit{true}.
To customize the diagram display, the developer can also settle the \textit{colors} option.
......@@ -322,42 +325,42 @@ 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 is able to present up to six lists in the classical representations.
Reaching this number, the presented diagrams are not proportional with the list counts and the intersection areas are often too small to display the
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.
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.
To present in a user-friendly manner five or six list diagrams, jvenn implements several functionnalities. First, the display can be switched to
To present in a user-friendly manner five or six list diagrams, jvenn implements 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 figures readibility on the classical six lists Venn graphic it was decided not to present all the values and to link some areas
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 behaviour 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 the figure and fades the others out.
Scientists are usually interested in extracting identifier lists from some of the intersections, therefore, jvenn implements an on click function which
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.
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
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.
jvenn performances depends on the client browser. Using the running version (link below) on a standard linux computer, it displays a six lists diagram of
jvenn's performance depends on the client browser. Using the running version (link below) on a standard linux computer, it displays a six lists diagram of
10 000 identifiers in two seconds.
As examples, we produced two venn diagrams representing six samples SRR068049, SRR06805, SRR068051, SRR068052, SRR068053 and
As examples, we produced two Venn diagrams representing six samples SRR068049, SRR06805, SRR068051, SRR068052, SRR068053 and
SRR068054 corresponding to sets of Operational Taxonomic Units observed under different conditions. Fig. 1 shows intersections
between the six of them using the classical Venn diagram display. In Fig. 2, jvenn overlights the intersection between three samples out of
between the six of them using the classical Venn diagram display. In Fig. 2, jvenn highlights the intersection between three samples out of
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.
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.
\section*{Availability and requirements}
......@@ -426,7 +429,7 @@ the system and for pointing out features worth developing.
\begin{figure}[h!]
\caption{\csentence{A six lists classic Venn diagram.}
This Venn diagram displays overlaps between six different biological samples. When
the user clicks on a figure, it calls the developper defined function.
the user clicks on a figure, it calls the developer 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. The charts showing the lists
......
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