Maintenance - Mise à jour mensuelle Lundi 1 Juin 2020 entre 7h00 et 9h00

Commit 52864607 authored by Jerome Mariette's avatar Jerome Mariette

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......@@ -284,14 +284,14 @@ http://bioinfo.genotoul.fr/jvenn.
\section*{Background}
Biological projects are increasingly producing samples to assess differences
between conditions or individuals. Thus, it is important to provide researchers
with effective visualization tools to explore and extract relevant differences
between data sets. Data analysis often leads to compare lists of biological
identifiers (gene names, operational taxonomic unit, ...).
List intersection results are commonly visualized using Venn diagrams
\cite{Venn1880} presenting shared and unshared identifier counts. They provide a
simple way to extract similarities and differences between the lists.
Biological experiments are often based on sample or condition comparison.
Thus, it is important to provide researchers with effective visualization
tools to explore and extract relevant differences between data sets. Data
analysis often leads to compare lists of biological identifiers (gene names,
Operational Taxonomic Unit (OTU), ...). List intersection results are commonly
visualized using Venn diagrams \cite{Venn1880} presenting shared and unshared
identifier counts. They provide a simple way to extract similarities and
differences between the lists.
Many Venn diagram software packages are already available. They can be classified
using their type : stand-alone, library, Web applications, JavaScript library and
......@@ -334,22 +334,29 @@ The installation documentation is included in the software package which can be
downloaded from http://bioinfo.genotoul.fr/jvenn.
The library provides an option to define the input type : \textit{series}. It
accepts three different values : lists, intersection counts and count lists.
They are all JSON objects. ``Lists'' contain for each input its label and an identifiers table.
``Intersection counts'' contain a correspondence table
accepts three different formats : lists, intersection counts and count lists.
All are JSON objects. ``Lists'' contain for each input label and an
identifiers table. ``Intersection counts'' contain a correspondence table
between labels and letters [A..F] and a table linking the 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 occurrence and their count.
Examples are presented in Table 1. In the case of list
or count lists \textit{series} jvenn 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 plug-in will only display the graphical result. The
display is based on a JavaScript canvas object allowing to export the chart as a
PNG file. The intersection table can also be downloaded as a CSV file.
It contains a header line with all diagram area labels and in column all the
identifiers of the elements contained in the area. These features can be disabled
by setting the \textit{exporting} option to \textit{false} hiding the exporting
button.
in which identifiers are replaced by their unique occurrence and their count.
Examples are presented in Table 1. Venn diagrams show intersections between a
collection of sets. However, in some cases it can be interested to display not
just the sets but also their counts. As example, an OTU represents a species or
a group of species given by a cluster leader of DNA sequences. Displaying such
data with the ``lists'' format leads to produce intersections of shared and
unshared OTUs between samples. However, using ``count lists'' allows to define
the amount of sequences constituting each OTUs. Thus, the produced diagram
represents the species abondance between samples.
For ``lists'' and ``count lists'' jvenn will first execute a function to compute
the intersections and display the chart. For ``intersection counts'', the
plug-in only displays graphic. The display is based on a JavaScript canvas
object allowing to export it as a PNG file. 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. These
features can be disabled by setting the \textit{exporting} option to
\textit{false} hiding the exporting button.
The Web application developer can also define the diagram display setting the
\textit{displayType} option to \textit{edwards} or \textit{classic}. Setting the
......@@ -357,17 +364,17 @@ The Web application developer can also define the diagram display setting the
of the plugin to substitute the intersection count by a question mark if this
one overflow its area. The callback function defining the click on an
intersection count can be overloaded by defining the \textit{fnClickCallback} parameter.
This function give 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
This function gives 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.
diagram display, the developer can also set the \textit{colors} option.
\section*{Results and Discussion}
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. This type of diagrams is able to present up
interested in using it with more. This type of diagram is able to present up
to six lists in its classical representation. Reaching this number, the
diagram can not a priori be proportional to the list counts and the intersection
areas are often too small to display the figures.
......@@ -379,7 +386,7 @@ enhance the figure's readability on the classical six lists Venn graphic, it was
to present all the values and to link some areas 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
and display the corresponding intersection counts. For all 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. Last, to show the
lists taking part in an intersection, jvenn highlights the corresponding areas on mouse over,
......@@ -389,8 +396,7 @@ Scientists are usually interested in extracting identifier lists from some of
the intersections, therefore, jvenn implements an one-click function which
retrieves the names of the corresponding samples and the identifiers. Seeking
an identifier can also be done using the plugin. The intersection with the
matching identifier is highlighted so the user can visualize the lists sharing
it.
matching identifier is highlighted as well as the lists containing it.
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)
......@@ -406,7 +412,7 @@ on a standard Linux computer (1 cpu, 4GB of RAM), it displays a six lists diagra
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 the six of them using the classical Venn diagram display.
intersections between all of them using the classical Venn diagram display.
In Fig. 2, jvenn highlights the intersection between three samples out of six
from an Edwards-Venn diagram.
......
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