diff --git a/covid_comp_bats.Rnw b/covid_comp_bats.Rnw
new file mode 100644
index 0000000000000000000000000000000000000000..08b9a62f0420ef963e9a20d0bb3498e08f7d6d14
--- /dev/null
+++ b/covid_comp_bats.Rnw
@@ -0,0 +1,113 @@
+\documentclass[11pt, oneside]{article} % use "amsart" instead of "article" for AMSLaTeX format
+%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
+%\geometry{letterpaper} % ... or a4paper or a5paper or ...
+%\geometry{landscape} % Activate for for rotated page geometry
+%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
+%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
+ % TeX will automatically convert eps --> pdf in pdflatex
+%\usepackage{amssymb}
+
+\usepackage[utf8]{inputenc}
+%\usepackage[cyr]{aeguill}
+%\usepackage[francais]{babel}
+%\usepackage{hyperref}
+
+
+\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
+\author{Marie Cariou}
+\date{janvier 2021} % Activate to display a given date or no date
+
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Data}
+
+Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
+
+<<>>=
+workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
+
+tab<-read.delim(paste0(workdir,
+ "covid_comp/covid_comp_complete.txt"), h=T, sep="\t")
+dim(tab)
+@
+
+\section{Comparison Bats}
+
+\subsection{Cooper-bats results VS DGINN-bats results}
+
+<<omegaM7M8bats>>=
+
+plot(tab$cooper.batsAverage_dNdS, as.numeric(as.character(tab$bats_omegaM0codeml)),
+ xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
+abline(0,1)
+@
+
+\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
+
+\textit{I don't think we have the omega values}
+
+\section{Overlap}
+
+\subsection{Data}
+
+<<subbats>>=
+tmp<-na.omit(tab[,c("Gene.name", "bats_codemlM7M8.p.value", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value", "bats_BUSTED", "bats_BppM1M2", "bats_BppM7M8", "bats_codemlM1M2", "bats_codemlM7M8")])
+
+tmp$bats_codemlM7M8.p.value<-as.numeric(as.character(tmp$bats_codemlM7M8.p.value))
+dim(tmp)
+@
+
+174 genes (present in the 3 experiments)
+
+\subsection{Mondrian}
+
+<<mondrianbats>>=
+library(Mondrian)
+
+monddata<-as.data.frame(tmp$Gene.name)
+monddata$bats_hawkins<-ifelse(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
+monddata$bats_cooper<-ifelse(tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
+
+
+dginntmp<-rowSums(cbind(tmp$bats_codemlM1M2=="Y", tmp$bats_codemlM7M8=="Y",
+tmp$bats_BppM1M2=="Y", tmp$bats_BppM7M8=="Y", tmp$bats_BUSTED=="Y"))
+
+monddata$bats_dginn<-ifelse(dginntmp>=3, 1,0)
+mondrian(monddata[,2:4], labels=c("DGINN >=3", "hawkins", "Cooper"))
+
+monddata$bats_dginn<-ifelse(dginntmp>=4, 1,0)
+mondrian(monddata[,2:4], labels=c("DGINN >=4", "hawkins", "Cooper"))
+@
+
+\subsection{subsetR}
+
+<<subsetbats>>=
+library(UpSetR)
+upsetdata<-as.data.frame(tmp$Gene.name)
+
+upsetdata$bats_hawkins<-ifelse(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
+upsetdata$bats_cooper<-ifelse(tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
+
+upsetdata$bats_dginn<-ifelse(dginntmp>=3, 1,0)
+
+upset(upsetdata, nsets = 3, matrix.color = "#DC267F",
+main.bar.color = "#648FFF", sets.bar.color = "#FE6100")
+
+upsetdata$bats_dginn<-ifelse(dginntmp>=4, 1,0)
+
+upset(upsetdata, nsets = 3, matrix.color = "#DC267F",
+main.bar.color = "#648FFF", sets.bar.color = "#FE6100")
+
+@
+
+
+
+
+
+\end{document}
+
diff --git a/covid_comp_bats.pdf b/covid_comp_bats.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..6a94749512a2dd3398e2d43fe5a4e2ae8ac14fd0
Binary files /dev/null and b/covid_comp_bats.pdf differ
diff --git a/covid_comp_bats.tex b/covid_comp_bats.tex
new file mode 100644
index 0000000000000000000000000000000000000000..1334ecaf9228485f664fcd2e54e7bc4385fa13c9
--- /dev/null
+++ b/covid_comp_bats.tex
@@ -0,0 +1,207 @@
+\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
+% maxwidth is the original width if it is less than linewidth
+% otherwise use linewidth (to make sure the graphics do not exceed the margin)
+\makeatletter
+\def\maxwidth{ %
+ \ifdim\Gin@nat@width>\linewidth
+ \linewidth
+ \else
+ \Gin@nat@width
+ \fi
+}
+\makeatother
+
+\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
+\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
+\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
+\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
+\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
+\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
+\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
+\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
+\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
+\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
+\let\hlipl\hlkwb
+
+\usepackage{framed}
+\makeatletter
+\newenvironment{kframe}{%
+ \def\at@end@of@kframe{}%
+ \ifinner\ifhmode%
+ \def\at@end@of@kframe{\end{minipage}}%
+ \begin{minipage}{\columnwidth}%
+ \fi\fi%
+ \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
+ \colorbox{shadecolor}{##1}\hskip-\fboxsep
+ % There is no \\@totalrightmargin, so:
+ \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
+ \MakeFramed {\advance\hsize-\width
+ \@totalleftmargin\z@ \linewidth\hsize
+ \@setminipage}}%
+ {\par\unskip\endMakeFramed%
+ \at@end@of@kframe}
+\makeatother
+
+\definecolor{shadecolor}{rgb}{.97, .97, .97}
+\definecolor{messagecolor}{rgb}{0, 0, 0}
+\definecolor{warningcolor}{rgb}{1, 0, 1}
+\definecolor{errorcolor}{rgb}{1, 0, 0}
+\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
+
+\usepackage{alltt} % use "amsart" instead of "article" for AMSLaTeX format
+%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
+%\geometry{letterpaper} % ... or a4paper or a5paper or ...
+%\geometry{landscape} % Activate for for rotated page geometry
+%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
+%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
+ % TeX will automatically convert eps --> pdf in pdflatex
+%\usepackage{amssymb}
+
+\usepackage[utf8]{inputenc}
+%\usepackage[cyr]{aeguill}
+%\usepackage[francais]{babel}
+%\usepackage{hyperref}
+
+
+\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
+\author{Marie Cariou}
+\date{janvier 2021} % Activate to display a given date or no date
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Data}
+
+Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{workdir}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"}
+
+\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"covid_comp/covid_comp_complete.txt"}\hlstd{),} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\hlkwd{dim}\hlstd{(tab)}
+\end{alltt}
+\begin{verbatim}
+## [1] 333 161
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\section{Comparison Bats}
+
+\subsection{Cooper-bats results VS DGINN-bats results}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0codeml)),}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-bats"}\hlstd{)}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in xy.coords(x, y, xlabel, ylabel, log): NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8bats-1}
+
+\end{knitrout}
+
+\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
+
+\textit{I don't think we have the omega values}
+
+\section{Overlap}
+
+\subsection{Data}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_codemlM7M8.p.value"}\hlstd{,} \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,} \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,} \hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{)])}
+
+\hlstd{tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlkwd{dim}\hlstd{(tmp)}
+\end{alltt}
+\begin{verbatim}
+## [1] 174 9
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+174 genes (present in the 3 experiments)
+
+\subsection{Mondrian}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(Mondrian)}
+
+\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+
+
+\hlstd{dginntmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tmp}\hlopt{$}\hlstd{bats_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN >=3"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"Cooper"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianbats-1}
+\begin{kframe}\begin{alltt}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN >=4"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"Cooper"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianbats-2}
+
+\end{knitrout}
+
+\subsection{subsetR}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(UpSetR)}
+\hlstd{upsetdata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
+
+\hlstd{upsetdata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{upsetdata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+
+\hlstd{upsetdata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+\hlkwd{upset}\hlstd{(upsetdata,} \hlkwc{nsets} \hlstd{=} \hlnum{3}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
+\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/subsetbats-1}
+\begin{kframe}\begin{alltt}
+\hlstd{upsetdata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+\hlkwd{upset}\hlstd{(upsetdata,} \hlkwc{nsets} \hlstd{=} \hlnum{3}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
+\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/subsetbats-2}
+
+\end{knitrout}
+
+
+
+
+
+\end{document}
+