Commit 1961ab1c authored by Jerome Mariette's avatar Jerome Mariette

last version paper

parent c0b95c28
......@@ -208,12 +208,12 @@ 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 Venn diagramm visualization features in WEB pages. jvenn is fully configurable and allows to control
and customize all user interactions.
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 some integration examples, is freely available at
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
https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
......@@ -284,7 +284,7 @@ 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 on WEB pages. Thus, several Venn diagram applications are
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
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
......@@ -292,11 +292,11 @@ API \cite{googleAPI}, meanwhile, are javascript libraries including Venn diagram
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
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 cited in several scientific
to overload the callback function in order to control users interactions. jvenn has already been cited in two scientific
publications \cite{Bianchia2013, Aravindraja2013}.
......@@ -308,12 +308,12 @@ WEB application at http://bioinfo.genotoul.fr/index.php?id=116. The installation
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
display the chart. In the case of intersection counts \textit{series}, the plugin will only display the graphical results. The resulting
display is based on the javascript canvas object allowing to export the chart as a PNG file. This last feature can be disabled in order
to hide the exporting button from the user by setting the \textit{exporting} option to \textit{false}.
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}
option to \textit{false} hiding the exporting button.
The WEB application developer can also overload the callback function defining the click on an overlap number. 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.
......@@ -323,42 +323,41 @@ To customize the diagram display, the developer can also settle the \textit{colo
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 too small to display the
Reaching this number, the presented diagrams are not proportional with 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
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
to their figures using lines. This did not permit to show all figures, therefore a switch button panel (Fig. 1) was added. This panel enables
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
retrieves the name of the corresponding samples and the identifiers.
retrieves the names of the corresponding samples and the identifiers.
Having an overview of the input data and comparing multiple diagrams can be difficult when using a Venn vizualisation. Thus, jvenn provides two extra
charts (Fig. 1) bellow the Venn diagram. The first one represents the input lists size histogram. It allows users to check the list size homogeneity.
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.
The second one, displays the number of elements located in intersections shared over 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
10 000 identifiers in two seconds.
jvenn performances depends on the client browser. Using the running version (link below) on a standard linux computer, it displays a six lists of 10 000
identifiers in two seconds.
As example, 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 six of them using the Venn diagram display. In Fig. 2, jvenn overlights the intersection between three samples out of
six.
between the six of them using the classical Venn diagram display. In Fig. 2, jvenn overlights 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
within a WEB page without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse
\cite{Mariette} and WallProtDB \cite{SanClemente} WEB applications.
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}
......
......@@ -50,10 +50,10 @@
The present cover letter is pertaining to the paper "jvenn: an interactive venn diagram viewer".
For 10 years we have been working in animal and plant genomics. Our aim has always been to provide biologists with a user friendly environment
to present the results in a simple but rich manner. With jvenn we provide a javascript library which can be included in any web-platform to
interactively explore Venn diagrams over a web browser without any further software barriers. This could be compared to the creation of Cytoscape-Web
and jHeatmap both published in Bioinformatics. jvenn is the only library able to handle up to 6 input lists presenting results as classical or
Edwards-Venn diagrams and has already been used in several scientific publications and web applications.
to present their results in a simple but rich manner. With jvenn we provide a javascript library which is embedable in any web-platform to
interactively display Venn diagrams. This could be compared to Cytoscape-Web or jHeatmap both published in Bioinformatics. jvenn is the only
library able to handle up to 6 input lists presenting results as classical or Edwards-Venn diagrams and has already been cited in two scientific
publications and is part of three web applications.
This paper is unpublished and has not been submitted for publication elsewhere.
We would be grateful if you would consider it for publication in BMC bioinformatics.
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