@@ -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.
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@@ -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
