Commit c0a87fea authored by Jerome Mariette's avatar Jerome Mariette
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......@@ -286,18 +286,18 @@ http://bioinfo.genotoul.fr/jvenn.
With the advent of high-throughput biology the number of compared samples,
within an experiment, is increasing. The analysis step often leads to the
production of a biological identifier list, such as gene names or operational
taxonomic units, for each sample. A common visualization chart is the Venn
diagrams \cite{Venn1880} which allows to spot shared and unshared identifiers
providing an insight on the similarities between the lists.
production of a biological identifier list, including gene names or operational
taxonomic units, for each sample. Venn diagrams \cite{Venn1880} are a common
visualization chart which allow to spot shared and unshared identifiers
providing an insight on lists similarities.
In a Venn diagram each list is figured by a transparent shape. Shape overlaps
In a Venn diagram each list is presented by a transparent shape. Shape overlaps
contain the elements shared between lists or more often the corresponding counts.
In proportional Venn diagrams the size of a shape depends on the number of
elements of the corresponding list intersection. Venn diagrams with up to four
lists are easy to read and understand, but they become difficult to interpret
with more lists. To solve this problem, the Edwards-Venn \cite{Edwards2004}
representation introduces new shapes providing a clearer view (Fig. 2).
lists are easy to read and understand, having more lists, they become difficult
to interpret. To solve this problem, the Edwards-Venn \cite{Edwards2004}
representation introduces new shapes providing a clearer view (Fig. 2).
Many Venn diagram software packages are already available. The first six lines
of Table 1 present a subset of selected packages with their features including
......@@ -305,11 +305,11 @@ maximum number of input lists, input data formats, Venn diagram layouts,
application types and output formats. The table gives insight on several aspects
of Venn diagram production and highlights that no WEB applications handle up to
six lists. VENNTURE \cite{Bronwen2012} is the only application able to
produce such diagrams but this one only implements Edwards layout and only runs
under MS-Windows to produce static MS-PowerPoint files. Proportional Venn
diagrams are very limited in the number of lists they can display : maximum
three. Therefore programs designed to display high number of lists will
implement non proportional diagrams.
produce such diagrams but it only implements Edwards layout and runs only
under MS-Windows producing static MS-PowerPoint and MS-Excel files. Proportional
Venn diagrams can only display very limited number of lists : maximum three.
Therefore programs designed to display high number of lists will implement non
proportional diagrams.
Hereafter we introduce jvenn, a JavaScript library, developed as a jQuery
plug-in \cite{jquery}, including many features easing diagram production and
......@@ -331,7 +331,7 @@ intersection names formed by the successions of letters and the counts. ``Count
lists'' are organized as ``Lists'' in which identifiers are replaced by their
unique occurrences and their counts. With ``Count lists'' the figures presented
in the diagram correspond to the sums of counts of all identifiers shared
between lists. This has been used in diversity studies to present OTU
between lists. They have been used in diversity studies to present OTU
(Operational Taxonomic Unit) read counts. For ``Lists'' and ``Count lists'',
jvenn computes the intersection counts and displays the chart. For
``intersection counts'', it only displays the graphic.
......@@ -339,8 +339,8 @@ jvenn computes the intersection counts and displays the chart. For
\subsection*{Display features}
Venn diagrams are commonly used to present up to six lists in its classical
representation. But then, the intersection areas are often too small to display
the figures.
representation. Reading six lists, 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 functionalities (Fig. 1). First, the display can be switched to
......@@ -360,13 +360,6 @@ comparison of multiple diagrams. The list size graph allows users to check the
homogeneity of the input list sizes. The intersection size graph can be used to
compare the compactness of multiple Venn diagrams.
For more than three lists diagrams, jvenn presents a switch button panel to
highlight intersections (Fig. 1). It also provides two extra charts (Fig. 1)
located bellow the Venn. The first one represents the input lists size
histogram. The second one displays the number of elements in intersections of a
certain size. It includes, as well, search and intersection identifiers export
functions.
Scientists are usually interested in extracting identifier lists for some
intersections, therefore, jvenn implements an one-click function which retrieves
the names of the corresponding sets and the identifiers. To find an identifier
......@@ -375,23 +368,27 @@ then highlighted.
\subsection*{Outputs}
The display is based on a JavaScript canvas object allowing PNG export. The
jvenn display is based on a JavaScript canvas object allowing PNG export. The
intersection table can also be downloaded as a CSV file. It contains a header
line with the diagram area labels and, in column, the identifiers of the
elements contained in the area. This feature can be customized by the
developper.
developer.
\subsection*{Integration}
jvenn allows programmers, with moderate JavaScript experiences to embed Venn
diagrams in a Web page without dependency. It has been designed following the
examples of jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010},
and jHeatmap \cite{DeuPons2014}.
The integration documentation is included in the software package which can be
downloaded from http://bioinfo.genotoul.fr/jvenn.
\subsection*{Web application}
To simply produce a Venn diagram from identifier lists, jvenn is
available as a Web application at http://bioinfo.genotoul.fr/jvenn/example.html
(Fig. 3).
The installation documentation is included in the software package which can be
downloaded from http://bioinfo.genotoul.fr/jvenn.
\subsection*{Performances}
jvenn's performance depends on the client browser. Using the running version
jvenn's Web application performances depends on the client browser. Using the running version
on a standard Linux computer (one cpu, 4GB of RAM), it displays a six lists
diagram of 10 000 identifiers in two seconds.
......@@ -402,9 +399,9 @@ M.A. Dillies and colleagues \cite{Dillies2012} have compared seven RNA-Seq data
normalization methods and given a set of best practices to help biologists in their
data processing. In table two, they have shown the differences between methods
pair-wise. The raw data table provided by the team contains 5,277 lines and
eight columns. The columns correspond to the different methods presented in the
seven columns. The columns correspond to the different methods presented in the
'Differential expression analysis' section of the article. The data in the table
was thresholded ($p < 0.05$) to produce the method specific gene name lists. Six
was threshold ($p < 0.05$) to produce the method specific gene name lists. Six
out of seven methods were selected for further processing ; Med was left out.
The lists were uploaded to the jvenn application and a Venn diagram was
produced. Using the layout selector the diagram was shown in Edwards Venn
......@@ -420,8 +417,8 @@ very different sizes (minimum 417 - maximum 1,249) and the most of the genes are
shared between methods : 1,069 genes out of 1,347 shared by at least four methods.
The same analysis was performed with VENNTURE, the only tool enabling to
generate a six list Edwards Venn diagram. First the software package was
installed on a computer running under MS-Windows. The six gene lists were loaded
generate a six list Edwards Venn diagram. First, the software package was
installed on a computer running under MS-Windows. Then, the six gene lists were loaded
in an MS-Excel spreadsheet. VENNTURE was run using the spreadsheet as input
generating a static MS-PowerPoint file containing the diagram and a MS-Excel
file with all the intersection contents. The names of 484 genes shared by DESeq,
......@@ -431,30 +428,26 @@ spreadsheet.
\section*{Discussion}
jvenn enables to compare up to six lists and dynamically to update the diagram
by modifying the list content. Compared to VENNTURE it does not need any
jvenn enables to compare up to six lists and updates the diagram automatically
when modifying the list content. Compared to VENNTURE it does not need any
installation and gives access to a dynamic diagram providing simple functions to
extract gene lists and perform searches.
jvenns' statistical charts give a simple and quick overview of the sizes of the
different lists and of their overlaps. This enables to compare different Venn diagrams.
These features are not available in the VENNTURE software package.
jvenns' statistical view gives a simple a quick overview of the sizes of the
different lists and of the overlaps. This enables to compare different Venn diagrams.
jvenn diagrams
dynamic : list extraction, identifier search
no statistical view
Multiple layouts
For biologists using different techniques in their experiment or in their statistical
analysis, jvenn enables to quickly extract the shared identifiers. Being found
using different approaches increases their confidence level.
\section*{Conclusions}
jvenn allows programers, with moderate JavaScript experiences to embed Venn
diagrams in a Web page without dependency. It has been designed following the
examples of jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010},
and jHeatmap \cite{DeuPons2014}.
Thanks' to the presented features, jvenn can be used in many cases to compare different
sets of results and easily extract the shared elements. Other examples, such as OTU
comparisons or bioinformatic software benchmarking results,
could complete the previously given ones.
jvenn can help to automate this kind of analysis while embedded in a Web environment as it has
been implemented in WallProtDB \cite{SanClemente}
\section*{Availability and requirements}
......
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