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BMC_jvenn/bmc_jvenn.tex

@@ -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.