Commit 7b2dac74 authored by Jerome Mariette's avatar Jerome Mariette
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parent 8c07b3da
...@@ -53,6 +53,17 @@ ...@@ -53,6 +53,17 @@
year = {2010} year = {2010}
} }
%%%%%%%%
% Complete book
%
@book{Edwards2004,
author = {Edwards, A.W.F.},
title = {Cogwheels of the Mind: The Story of Venn Diagrams.},
publisher = {Johns Hopkins University Press},
year = {2004},
address = {Baltimore}
}
%%%%%%%% %%%%%%%%
% Webpage Link / URL % Webpage Link / URL
% %
...@@ -70,3 +81,8 @@ ...@@ -70,3 +81,8 @@
title = {The canvasxpress venn diagram functionalities.}, title = {The canvasxpress venn diagram functionalities.},
url = {http://canvasxpress.org/venn.html} url = {http://canvasxpress.org/venn.html}
} }
@webpage{googleAPI,
title = {The Google chart API.},
url = {https://developers.google.com/chart/}
}
...@@ -178,45 +178,11 @@ ...@@ -178,45 +178,11 @@
\begin{abstract} % abstract \begin{abstract} % abstract
\parttitle{Background} %if any \parttitle{Background} %if any
In many genomics projects, numerous lists containing biological identifiers are produced. Often
it is useful to see the overlap between different lists, enabling researchers to quickly observe
similarities and differences between the data sets they are analyzing. One of the most popular
methods to visualize the overlap and differences between data sets is the Venn diagram: a diagram
consisting of two or more circles in which each circle corresponds to a data set, and the overlap
between the circles corresponds to the overlap between the data sets. Venn diagrams are especially
useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond
to the sizes of the data sets. Currently there are no programs available that can create area-proportional
Venn diagrams connected to a wide range of biological databases.
The generation of large volumes of omics data to
conduct exploratory studies has become feasible and is now
extensively used to gain new insights in life sciences. The effective
exploration of the generated data by experts is a crucial step for the
successful extraction of knowledge from these data sets. This
requires availability of intuitive and interactive visualization tools
which can display complex data. Matrix heatmaps are graphical
representations frequently used for the description of complex omics
data. Here we present jHeatmap, a web-based tool which allows
interactive matrix heatmap visualization and exploration. It is an
adaptable javascript library designed to be embedded by means of
basic coding skills into web-portals to visualize data matrices as
interactive and customizable heatmaps.
\parttitle{Results} %if any \parttitle{Results} %if any
We designed a web application named BioVenn to summarize the overlap between two or three lists of
identifiers, using area-proportional Venn diagrams. The user only needs to input these lists of
identifiers in the textboxes and push the submit button. Parameters like colors and text size can
be adjusted easily through the web interface. The position of the text can be adjusted by 'drag-and-drop'
principle. The output Venn diagram can be shown as an SVG or PNG image embedded in the web application,
or as a standalone SVG or PNG image. The latter option is useful for batch queries. Besides the Venn diagram,
BioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as
belonging to one of the supported biological databases, the output is linked to that database. Finally,
BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes.
\parttitle{Conclusions} %if any \parttitle{Conclusions} %if any
jquery.venny is an easy-to-use web application to generate Venn and Edward diagrams from lists of
biological identifiers. Its implementation on the World Wide Web makes it available for use on any computer
with internet connection, independent of operating system and without the need to install programs locally.
The software package is freely available under the GNU General Public License (GPL) at The software package is freely available under the GNU General Public License (GPL) at
https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil. Examples and the documentation https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil. Examples and the documentation
can be found on the sources directory and a running version is running at http://bioinfo.genotoul.fr/index.php?id=116. can be found on the sources directory and a running version is running at http://bioinfo.genotoul.fr/index.php?id=116.
...@@ -280,122 +246,35 @@ can be found on the sources directory and a running version is running at http:/ ...@@ -280,122 +246,35 @@ can be found on the sources directory and a running version is running at http:/
%% %%
\section*{Background} \section*{Background}
In many genomics projects and other projects handling large amounts of biological data, various lists
containing biological identifiers are produced, corresponding to e.g. sets of genes regulated under different
treatments. Often, it is useful to see the overlap between these lists. This enables researchers to quickly
observe similarities and differences between the data sets they are analyzing. One of the most popular methods
to visualize the overlap and differences between data sets is the Venn diagram, named by its inventor John Venn
\cite{Venn1880}. A large number of different types of Venn diagrams exist, the most popular being the three-circle
Venn diagram, used to visualize the overlap between three data sets. In such a diagram, the size of the circle can
be used to represent the size of the corresponding data set. This is called an area-proportional Venn diagram
[2]. Venn diagrams have been used recently to visualize gene lists [3,4]. However, these applications generate
diagrams with circles of equal size.
There are some computer programs available that generate area-proportional Venn Diagrams, either as rectangles
[5] or as polygons [6]. Drawback of these programs is that they need to be downloaded and run locally, limiting
their use by a wide community. There is also the Google Chart API [7], which can generate circular, area-proportional
Venn Diagrams, but can only have three numbers as input, and cannot do any calculations to obtain these three numbers.
There is currently no web application available that can generate circular, area-proportional Venn diagrams connected
to a wide range of biological databases, and can map different kinds of IDs to genes. In this article, we present a
web application named BioVenn which can generate circular, area-proportional Venn diagrams just by entering two or
three lists of biological IDs. IDs that can be recognized by BioVenn as belonging to a certain database, are linked
to that database. BioVenn currently supports cross-references to Affymetrix [8], COG [9], Ensembl [10], EntrezGene [11],
Gene Ontology [12], InterPro [13], IPI [14], KEGG Pathway [15], KOG [16], PhyloPat [17] and RefSeq [18]. BioVenn is based
on a previous version [19], which has been used in several scientific publications to visualize sets and their overlapping
areas [20-22].
The need for effective tools for data visualization is rising with the
increasing data volumes generated by scientific studies. Effective
data visualization lets the researcher understand his/her data at
both broad and detailed levels and enables barrier-free exploration
of the data sets. A widely used type of visualization to report
biological results are matrix heatmaps, that represent a data set
with two dimensions, commonly genes and samples. The values in
the matrix may represent any widely measurable property such as
expression values. The static nature of such plots is a limiting
factor in order to explore complex data sets. Therefore we
introduced the use of interactive heatmaps and developed Gitools,
a desktop application for this purpose (Perez-Llamas and Lopez-
Bigas, 2011). With jHeatmap we provide a javascript library which
can be included in any web-platform to interactively explore
heatmaps over a web browser without any further software
barriers. This could be compared to the creation of Cytoscape-Web
(Lopes et al., 2010) which maintains basic features for
network visualization of Cytoscape desktop application. The
data is visualized in a heatmap matrix that can contain multiple
values per cell and thus allows loading multidimensional data sets
such as alteration data from oncogenomic study cohorts. Each cell
is associated to two features, e.g. genes and samples, with
additional information, e.g. clinical information for samples, and a
set of values. Columns and rows can be moved freely, and can be
filtered and sorted based on values in the cells or based on
annotations. All of properties associated to rows and columns can
be color coded or printed as text.
\section*{Implementation} The massive amounts of data generated by biological projects makes the analysis of such projects more and
a jquery plugin more difficult. In such a context, it is important to provide researchers with effective visualization
all figures are a canvas object tools to explore and extract relevant knowledge from these data sets. Data analysis often leads to the
The jquery.venny main features are: up to 6 classes venn diagram, allow to display Edwards-Venn diagram, easily integrable production of biological identifiers (gene names, operational taxonomic unit, ...) for which it is
within your own web site, 3 different ways to provide the data (list/number/list+number), control the click callback function, interesting to know intersections between samples. One of the most popular visualization chart is the
export the venn diagram to PNG. Venn diagrams \cite{Venn1880} wich allows to identify shared and unshared identifiers providing an insight
on the similarities between the data sets.
jHeatmap is a JavaScript plugin for jQuery and only has to be
referenced from within a HTML file with the necessary Several Venn diagram applications are availble. Some of them such as BioVenn \cite{Hulsen2008} or venny
configuration linking the data matrix file and the visualization \cite{venny} provides their users a web application with text areas as inputs to enter identifiers.
options. The browser will load the data and draw the heatmap in Where the first one outputs a three lists area-proportional diagram, the second one offers a four lists
the web browser as desired. diagram without any respect of area proportions. Canvasxpress \cite{canvasxpress} and the Google Chart API
As depicted in Figure 1, the heatmap has four components: The \cite{googleAPI}, meanwhile, are javascript libraries including Venn diagram features that can easily be
matrix heatmap, labels and color annotations for columns on top embedded in any WEB site. These libraries can only have as inputs numbers corresponding to each intersections
and for rows to the left and right and finally a control area on the and cannot perform any calculations to otain them.
top left. In the control area the user may select what value is
displayed in case the cells, rows or columns are associated with We intruduce jvenn a javascript library aiming to be part of rich WEB environments helping scientists to analyse
multiple values. For each of the three areas, a drop-down menu their data, such does already existing tools as jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010},
reveals to the user the different values that are available for cells, and jHeatmap \cite{DeuPons2014}. Jvenn handles up to 6 lists venn diagram, can display Edwards-Venn diagram
rows or columns respectively. Columns and rows can be selected, \cite{Edwards2004}, can easily be embeded within any web site, allows to provide inputs data from three different ways
moved, sorted and hidden which gives the user great flexibility to (list/number/list+number), provides a feature to export the diagram to png and allows to overload the callback
focus on the data points of interest. Columns and rows can be function to control users interactions. jvenn has already been used in several scientific publications to display
selected by click and drag actions. Clicking on ♦ will sort the sets and their overlapping areas \cite{Bianchia2013, Aravindraja2013}.
matrix by the selected rows or columns. Rows and columns used
for sorting will be labeled with triangles (▲ ▼) indicating the
ordering applied, and clicking them will toggle the direction. The
row and column annotations offer the same possibility. Further
interactions can be accessed through a contextual menu revealed
by a long click on the row or column labels.
jHeatmap is designed for incorporation into web portals and
applications. Documentation about several extension points can be
found at the jHeatmap website.
\section*{Results and Discussion}
Given the possibility to generate large amount of biological data \section*{Implementation}
with high-throughput technologies the need for data visualization
and analysis in biology is increasing. The shift from hypothesisdriven
to data-driven analyses requires field experts to directly
access the data. The visual and interactive access to complex data
enables experts to reason and decide over further analytical
procedures. For example in cancer genomics researchers need to
visualize and analyze complex multidimensional genomic data
often of large number of patients (Schroeder et al., 2013). For the
above stated reasons we present the jHeatmap software library for
easy representation of big data sets. jHeatmap is already in use
within the IntOGen platform (Gundem et al., 2010; Gonzalez-
Perez et al., 2013), the Achilles Project (Cheung et al., 2011) and
GenomeSpace (Liefeld, 2013) web platforms. jHeatmap is open
source, reusable and extendable: the web creator may easily
include the library to existing projects in order to visualize
multidimensional data sets of any size. Basic coding skills are
required. For more advanced users it is possible to adapt and
extend the code as needed.
With jHeatmap, we complement already existing stand-alone
desktop solutions for interactive heatmaps such as Gitools (Perez-
Llamas and Lopez-Bigas, 2011) or Java TreeView (Saldanha,
2004) with an open source matrix heatmap visualizer prepared for
integration into webs. jHeatmap offers a set of actions to provide
an interactivity that allows the user to visually mine the data:
According to the defined software interactions (Yi et al., 2007)
jHeatmap lets the user select, explore, reconfigure, encode and
filter rows, columns and cells of the heatmap.
\section*{Results and Discussion}
\subsection*{How to embed jquery.venny in your own web application} \subsection*{How to embed jquery.venny in your own web application}
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