Commit 2de43ac2 authored by Jerome Mariette's avatar Jerome Mariette

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parent a1b2d1eb
......@@ -516,12 +516,51 @@ reviewers for their insightful and constructive comments.
%% Use of \listoftables is discouraged.
%%
\section*{Tables}
\begin{table}[h!]
\caption{Available formats and example for the \textit{series} option.}
\begin{tabular}{c|cccccc}
Application & Maximum & Layouts & Application &
Proportionality & Input data & Output\\
& number of & & type & & formats & formats \\
& input lists & & & & & \\ \hline
VENNTURE \cite{Bronwen2012} & 6 & Edwards & Stand-alone & No & Lists &
Powerpoint,\\
& & & & & & Excel, CSV \\ \hline
VennDiagram \cite{RVennDiagram} & 5 & Classical & R package & No & Lists
& R object, TIFF \\ \hline
BioVenn \cite{Hulsen2008} & 3 & Classical & Web application & Yes &
Lists & SVG, PNG \\ \hline
venny \cite{venny} & 4 & Classical & Web application & No &
Lists & PNG \\ \hline
Canvasxpress \cite{canvasxpress} & 4 & Classical & JavaScript library &
No & Intersection counts & JavaScript canvas \\ \hline
Google & 3 & Classical & JavaScript library &
Yes & Lists & PNG \\
Chart API \cite{googleAPI} & & & & & & \\ \hline
jvenn & 6 & Classical & Web application & No & Lists,
& Interactive
\\
& & and Edwards & and JavaScript library & & intersection counts & diagram, \\
& & & & & and count lists & PNG, CSV
\end{tabular}
\end{table}
\begin{table}[h!]
\caption{Available formats and example for the \textit{series} option.}
\begin{tabular}{cccc}
\hline
format & example\\ \hline
lists &
Format & Example\\ \hline
Lists &
\begin{lstlisting}
series: [{
name: 'sample1',
......@@ -531,15 +570,16 @@ series: [{
data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"]
}]
\end{lstlisting}\\ \hline
intersection counts &
Intersection counts &
\begin{lstlisting}
series: [{
name: {A: 'sample 1', B: 'sample 2'},
data: {A: ["Otu3", "Otu4", "Otu6"], B: ["Otu8", "Otu9"], AB: ["Otu1",
"Otu2", "Otu5", "Otu7"]} }],
"Otu2", "Otu5", "Otu7"]},
values: {A: 3, B: 2, AB: 4}
}]
\end{lstlisting}\\ \hline
count lists &
Count lists &
\begin{lstlisting}
series: [{
name: 'sample1',
......
......@@ -51,7 +51,7 @@ The present cover letter is pertaining to the paper "jvenn: an interactive venn
diagram viewer". This paper has already been submitted to BMC Bioinformatics
under the ID 1449643681123201. After the review process, we were asked to
solve the concerns addressed. We made the requested modifications and we added
new features to jvenn presented in the manuscripts. Hereafter are our responses
new features to jvenn presented in the manuscript. Hereafter are our answers
to the reviewers.
......@@ -68,6 +68,7 @@ The URL have been changed to fit the page size.
\textbf{- run-on sentences}
The organisation of the sections and paragraphs of the text has been modified.
Many sentences have been rewritten.
\textbf{- what is a standard linux computer?}
......@@ -127,7 +128,7 @@ not directly embeddable in a webpage. Yet, the authors should note these
libraries as well. Two that come to mind are: The VennDiagram R package, which
supports up to five lists. VENNTURE, which supports up to six lists Martin B,
Chadwick W, Yi T, Park SS, Lu D, Ni B, Gadkaree S, Farhang K, Becker KG,
Maudsley S. VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple
Maudsley S. VENNTURE Novel Venn Diagram Investigational Tool for Multiple
Pharmacological Dataset Analysis.}
These 2 citations and the description of the tools have been added in the
......@@ -139,7 +140,7 @@ diagrams with up to six lists; thus their statement is incorrect.}
VENNTURE citation has been added to the manuscript. jvenn remains the only
tools handling 6 lists as inputs written to be included in Web applications.
Moreover it is the only software offering the classical Venn diagram displays
Moreover it is the only software package offering classical Venn diagram displays
for 6 input lists.
\textbf{Also the authors point out that venny does not visualize the relative
......@@ -147,7 +148,7 @@ areas of the intersecting sets; neither does jvenn, from what I can
tell. Is this a current limitation of jvenn or an explicit decision?}
This is right, all softwares displaying a relative areas Venn diagram handle up
to 3 lists. Beyond that, displaying the graphic is a more complex problem.
to 3 lists. Beyond that, displaying the graphic is a complex problem.
\textbf{3. The jvenn library appears to be built upon the venny library;
however this distinction is unclear. In the implementation section,
......@@ -157,8 +158,8 @@ sets of items. A clear statement about the novel contributions (with
respect to the library) will strengthen the paper.}
jvenn is only using the venny algorithm to compute the lists intersection.
The sentence ``jvenn is based on venny regarding the algorithm computing the
lists intersections. The algorithm has been wrapped in a jQuery plug-in,
The sentence ``jvenn intersection computing algorithm is based on venny.
The algorithm has been wrapped in a jQuery plug-in,
extended with new features presented hereunder and the ability to use up to six
lists.'' has been added as introduction to the Implementation section.
......@@ -296,4 +297,4 @@ bioinformatics.
%----------------------------------------------------------------------------------------
\end{newlfm}
\end{document}
\end{document}
\ No newline at end of file
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