Commit 500fa6fd authored by Jerome Mariette's avatar Jerome Mariette
Browse files

venny > jvenn

parent 23d74719
......@@ -96,7 +96,7 @@
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\title{jvenny: an interactive venn diagram viewer.}
\title{jvenn: an interactive venn diagram viewer.}
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......@@ -188,6 +188,20 @@ useful when they are 'area-proportional' i.e. the sizes of the circles and the o
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
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
......@@ -200,11 +214,12 @@ belonging to one of the supported biological databases, the output is linked to
BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes.
\parttitle{Conclusions} %if any
BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of
biological identifiers. It supports a wide range of identifiers from the most used biological databases
currently available. Its implementation on the World Wide Web makes it available for use on any computer
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.
BioVenn is freely accessible at http://www.cmbi.ru.nl/cdd/biovenn/ webcite.
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
can be found on the sources directory and a running version is running at http://bioinfo.genotoul.fr/index.php?id=116.
\end{abstract}
......@@ -289,15 +304,102 @@ Gene Ontology [12], InterPro [13], IPI [14], KEGG Pathway [15], KOG [16], PhyloP
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}
a jquery plugin
all figures are a canvas object
The jquery.venny main features are: up to 6 classes venn diagram, allow to display Edwards-Venn diagram, easily integrable
within your own web site, 3 different ways to provide the data (list/number/list+number), control the click callback function,
export the venn diagram to PNG.
jHeatmap is a JavaScript plugin for jQuery and only has to be
referenced from within a HTML file with the necessary
configuration linking the data matrix file and the visualization
options. The browser will load the data and draw the heatmap in
the web browser as desired.
As depicted in Figure 1, the heatmap has four components: The
matrix heatmap, labels and color annotations for columns on top
and for rows to the left and right and finally a control area on the
top left. In the control area the user may select what value is
displayed in case the cells, rows or columns are associated with
multiple values. For each of the three areas, a drop-down menu
reveals to the user the different values that are available for cells,
rows or columns respectively. Columns and rows can be selected,
moved, sorted and hidden which gives the user great flexibility to
focus on the data points of interest. Columns and rows can be
selected by click and drag actions. Clicking on ♦ will sort the
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
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.
\subsection*{How to embed jquery.venny in your own web application}
\subsection*{How to use the our web application}
\subsection*{How to use our web application}
\section*{Conclusions}
......
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