diff --git a/covid_comp_dataset.Rnw b/covid_comp_dataset.Rnw
index 43510b4b3d34863d6c74f62e91baa1308b3ca524..13d3d3638a1697fef091015ae6c7fcd739281eb1 100644
--- a/covid_comp_dataset.Rnw
+++ b/covid_comp_dataset.Rnw
@@ -322,9 +322,8 @@ library(ggraph)
library(igraph)
library(tidyverse)
-##
tmp<-tablo[(tablo$nbats!=0 | tablo$nprimates!=0),]
-tmp<-head(tablo, 20)
+#tmp<-head(tablo, 20)
#tmp<-rbind(as.matrix(tmp), c("outgroup", 50, 50))
tmp<-as.data.frame(tmp)
matbats<-hclust(dist(tmp$nbats))
diff --git a/covid_comp_maic.Rnw b/covid_comp_maic.Rnw
new file mode 100644
index 0000000000000000000000000000000000000000..91fe81c5024fa40fe1b21c10e91ffae54f2935b3
--- /dev/null
+++ b/covid_comp_maic.Rnw
@@ -0,0 +1,280 @@
+\documentclass[11pt, oneside]{article} % use "amsart" instead of "article" for AMSLaTeX format
+%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
+%\geometry{letterpaper} % ... or a4paper or a5paper or ...
+%\geometry{landscape} % Activate for for rotated page geometry
+%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
+%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
+ % TeX will automatically convert eps --> pdf in pdflatex
+%\usepackage{amssymb}
+
+\usepackage[utf8]{inputenc}
+%\usepackage[cyr]{aeguill}
+%\usepackage[francais]{babel}
+%\usepackage{hyperref}
+
+
+\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis, maic}
+\author{Marie Cariou}
+\date{March 2021} % Activate to display a given date or no date
+
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Data}
+
+output from covid\_comp\_dataset.
+
+<<>>=
+tablo<-read.table("primatesVbats.csv",
+ h=T, sep=",")
+@
+
+Output MAIC formatted by Léa. This table includes the DGINN "score".
+
+<<>>=
+home<-"/home/adminmarie/Documents/"
+workdir<-paste0(home, "CIRI_BIBS_projects/2020_05_Etienne_covid/")
+maic<-read.table(paste0(workdir, "data/covid_comp_maic.txt"),
+ h=T)
+@
+
+\section{MAIC}
+
+\subsection{Boxplot}
+
+<<boxplot, fig.height=12>>=
+par(mfrow=c(2,1))
+boxplot(maic$rank~maic$nbats, notch=TRUE, varwidth=TRUE, xlab="score DGINN", ylab="rank MAIC", main="Bats")
+stripchart(maic$rank~maic$nbats, method="jitter", vertical=TRUE, pch=1, cex=0.3, add=TRUE)
+
+boxplot(maic$rank~maic$nprimates, notch=TRUE, xlab="score DGINN", ylab="rank MAIC", main="Primates")
+stripchart(maic$rank~maic$nprimates, method="jitter", vertical=TRUE, pch=1, cex=0.3, add=TRUE)
+@
+
+\subsection{Dotchart}
+
+<<dotbats, fig.height=8>>=
+tmp<-maic[maic$nbats>=3, c("gene", "rank", "nbats")]
+tmp<-tmp[order(tmp$rank, decreasing = TRUE),]
+tmp$col<-"black"
+tmp$col[tmp$gene=="ACE2"]<-"red"
+tmp$col[tmp$gene=="TMPRSS2"]<-"red"
+
+tmp$pch[tmp$nbats==5]<-1
+tmp$pch[tmp$nbats==4]<-20
+tmp$pch[tmp$nbats==3]<-4
+
+dotchart(tmp$rank, main="Bats DGINN >=3", xlab="rank MAIC", labels=tmp$gene, pch=tmp$pch, col=tmp$col)
+legend("topright", c("5 (score DGINN)", "4", "3"), pch=c(1,20,4))
+@
+
+<<dotprimates, fig.height=12>>=
+tmp<-maic[maic$nprimates>=3, c("gene", "rank", "nprimates")]
+tmp<-tmp[order(tmp$rank, decreasing = TRUE),]
+
+tmp$pch[tmp$nprimates==5]<-1
+tmp$pch[tmp$nprimates==4]<-20
+tmp$pch[tmp$nprimates==3]<-4
+tmp$col<-"black"
+tmp$col[tmp$gene=="ACE2"]<-"red"
+tmp$col[tmp$gene=="TMPRSS2"]<-"red"
+
+dotchart(tmp$rank, main="Primates DGINN >=3", xlab="rank MAIC", labels=tmp$gene, pch=tmp$pch, cex=0.8, col=tmp$col)
+legend("topright", c("5 (score DGINN)", "4", "3"), pch=c(1,20,4))
+
+@
+
+\section{Tanglegram}
+
+<<eval=FALSE>>=
+#install.packages('dendextend') # stable CRAN version
+library(dendextend) # load the package
+#install.packages("phytools") # stable CRAN version
+library(phytools) # load the package
+library(ggraph)
+library(igraph)
+library(tidyverse)
+
+##
+tmp<-tablo[(tablo$nbats!=0 | tablo$nprimates!=0),]
+tmp<-head(tablo, 20)
+#tmp<-rbind(as.matrix(tmp), c("outgroup", 50, 50))
+tmp<-as.data.frame(tmp)
+matbats<-hclust(dist(tmp$nbats))
+matpri<-hclust(dist(tmp$nprimates))
+
+
+tmp[order(tmp$nbats),]
+
+dendpri<-as.dendrogram(matpri)
+dendbats<-as.dendrogram(matbats)
+
+labels(dendpri)<-as.character(tmp$tmp.Gene.name[labels(dendpri)])
+labels(dendbats)<-as.character(tmp$tmp.Gene.name[labels(dendbats)])
+
+
+tmp[order(tmp$nprimates, decreasing=FALSE),]$tmp.Gene.name-> order
+dendpri<-dendextend::rotate(dendpri, order=order)
+
+tmp[order(tmp$nbats, decreasing=FALSE),]$tmp.Gene.name-> order
+dendbats<-dendextend::rotate(dendbats, order=order)
+
+#### Il faut swapper certains neuds de l'arbres
+
+
+class(labels(dendpri))
+
+dend12 <- dendlist(dendbats, dendpri)
+
+ace<-264
+tmprss2<-75
+znf318<-81
+sepsecs<-228
+tbk1<-273
+ripk1<-224
+
+col<-rep("grey", length(labels(dendpri)))
+col[ace]<-"black"
+col[tmprss2]<-"black"
+col[znf318]<-"black"
+col[sepsecs]<-"black"
+col[tbk1]<-"black"
+col[ripk1]<-"black"
+
+font<-rep(1, length(labels(dendpri))*2)
+#font[ace]<-1.3
+#font[tmprss2]<-1.3
+#font[length(labels(dendpri))+160]<-1.3
+
+png("tanglegramm.png", width = 1800, height = 3000)
+tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
+ edge.lwd=0, margin_inner=6,
+ margin_top=2,
+ main_left=" bats",
+ main_right = "primates ",
+ lwd=0.5,
+ cex_main=1,
+ lab.cex=font,
+ k_labels=6,
+ color_lines=col)
+
+dev.off()
+
+@
+
+
+<<>>=
+tmp<-tablo[(tablo$nbats>=3 | tablo$nprimates>=3),]
+dim(tmp)
+tmp<-as.data.frame(tmp)
+matbats<-hclust(dist(tmp$nbats))
+matpri<-hclust(dist(tmp$nprimates))
+#tmp[order(tmp$nbats),]
+
+dendpri<-as.dendrogram(matpri)
+dendbats<-as.dendrogram(matbats)
+
+labels(dendpri)<-as.character(tmp$tmp.Gene.name[labels(dendpri)])
+labels(dendbats)<-as.character(tmp$tmp.Gene.name[labels(dendbats)])
+
+tmp[order(tmp$nprimates, decreasing=FALSE),]$tmp.Gene.name-> order
+dendpri<-dendextend::rotate(dendpri, order=order)
+
+tmp[order(tmp$nbats, decreasing=FALSE),]$tmp.Gene.name-> order
+dendbats<-dendextend::rotate(dendbats, order=order)
+
+#### Il faut swapper certains neuds de l'arbres
+class(labels(dendpri))
+
+dend12 <- dendlist(dendbats, dendpri)
+
+ace<-97
+tmprss2<-27
+znf318<-31
+sepsecs<-69
+tbk1<-106
+ripk1<-68
+
+col<-rep("grey", length(labels(dendpri)))
+
+
+
+plusplus<-tmp$tmp.Gene.name[tmp$nbats>=3 & tmp$nprimates>=3]
+col[which(labels(dendbats) %in% plusplus)]<-"pink"
+
+interest<-c("TMPRSS2","ZNF318", "SEPSECS","TBK1", "RIPK1")
+col[which(labels(dendbats) %in% interest)]<-"black"
+
+interestpp<-c("ACE2")
+col[which(labels(dendbats) %in% interestpp)]<-"red"
+#col[ace]<-"black"
+#col[tmprss2]<-"black"
+#col[znf318]<-"black"
+#col[sepsecs]<-"black"
+#col[tbk1]<-"black"
+#col[ripk1]<-"black"
+
+png("tanglegrammsup3.png", width = 500, height = 1200)
+tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
+ edge.lwd=0, margin_inner=6,
+ margin_top=3,
+ main_left=" bats",
+ main_right = "primates ",
+ lwd=0.5,
+ cex_main=2,
+ lab.cex=1,
+ k_labels=6,
+ color_lines=col)
+
+dev.off()
+
+### Changer couleurs des groupes
+## changer couleurs des lines sel vs sel or sel vs non-sel
+
+setEPS()
+postscript("tanglegramsup3.eps", height=15, width=5)
+tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
+ edge.lwd=0, margin_inner=6,
+ margin_top=3,
+ main_left=" bats",
+ main_right = "primates ",
+ lwd=0.5,
+ cex_main=2,
+ lab.cex=1,
+ # k_labels=6,
+ color_lines=col)
+dev.off()
+
+
+labels_colors(dend12[[1]])<-rep(rainbow(15)[c(1:3, 9:11)], table(tmp$nbats))
+labels_colors(dend12[[2]])<-rep(rainbow(15)[c(1:3, 9:11)], table(tmp$nprimates))
+
+
+labels_colors(dend12[[1]])<-rep(viridis(10)[c(1:3, 7:9)], table(tmp$nbats))
+labels_colors(dend12[[2]])<-rep(viridis(10)[c(1:3, 7:9)], table(tmp$nprimates))
+setEPS()
+postscript("tanglegramsup3_V2.eps", height=15, width=5)
+tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
+ edge.lwd=0, margin_inner=6,
+ margin_top=3,
+ main_left=" bats",
+ main_right = "primates ",
+ lwd=0.5,
+ cex_main=2,
+ lab.cex=1,
+ # k_labels=6,
+ color_lines=col)
+dev.off()
+
+@
+
+
+\end{document}
+
+
+
+
diff --git a/covid_comp_maic.pdf b/covid_comp_maic.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..6c796ce9abad24172b8eaa481340255c34927ec4
Binary files /dev/null and b/covid_comp_maic.pdf differ
diff --git a/covid_comp_maic.tex b/covid_comp_maic.tex
new file mode 100644
index 0000000000000000000000000000000000000000..db9676a07af0db43c2eb59a4f8662864582a333c
--- /dev/null
+++ b/covid_comp_maic.tex
@@ -0,0 +1,239 @@
+\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, maic}
+\author{Marie Cariou}
+\date{March 2021} % Activate to display a given date or no date
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Data}
+
+output from covid\_comp\_dataset.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tablo}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlstr{"primatesVbats.csv"}\hlstd{,}
+ \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+Output MAIC formatted by Léa. This table includes the DGINN "score".
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{home}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/"}
+\hlstd{workdir}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"CIRI_BIBS_projects/2020_05_Etienne_covid/"}\hlstd{)}
+\hlstd{maic}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{"data/covid_comp_maic.txt"}\hlstd{),}
+ \hlkwc{h}\hlstd{=T)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\section{MAIC}
+
+\subsection{Boxplot}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{par}\hlstd{(}\hlkwc{mfrow}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{2}\hlstd{,}\hlnum{1}\hlstd{))}
+\hlkwd{boxplot}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nbats,} \hlkwc{notch}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{varwidth}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"score DGINN"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Bats"}\hlstd{)}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in bxp(list(stats = structure(c(21, 825, 1664, 2860, 5392, 15, 625.5, : some notches went outside hinges ('box'): maybe set notch=FALSE}}\begin{alltt}
+\hlkwd{stripchart}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nbats,} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{vertical}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.3}\hlstd{,} \hlkwc{add}\hlstd{=}\hlnum{TRUE}\hlstd{)}
+
+\hlkwd{boxplot}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nprimates,} \hlkwc{notch}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"score DGINN"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Primates"}\hlstd{)}
+\hlkwd{stripchart}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nprimates,} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{vertical}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.3}\hlstd{,} \hlkwc{add}\hlstd{=}\hlnum{TRUE}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/boxplot-1}
+
+\end{knitrout}
+
+\subsection{Dotchart}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tmp}\hlkwb{<-}\hlstd{maic[maic}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"gene"}\hlstd{,} \hlstr{"rank"}\hlstd{,} \hlstr{"nbats"}\hlstd{)]}
+\hlstd{tmp}\hlkwb{<-}\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{decreasing} \hlstd{=} \hlnum{TRUE}\hlstd{),]}
+\hlstd{tmp}\hlopt{$}\hlstd{col}\hlkwb{<-}\hlstr{"black"}
+\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"ACE2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
+\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
+
+\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{5}\hlstd{]}\hlkwb{<-}\hlnum{1}
+\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlnum{20}
+\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{3}\hlstd{]}\hlkwb{<-}\hlnum{4}
+
+\hlkwd{dotchart}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{main}\hlstd{=}\hlstr{"Bats DGINN >=3"}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{labels}\hlstd{=tmp}\hlopt{$}\hlstd{gene,} \hlkwc{pch}\hlstd{=tmp}\hlopt{$}\hlstd{pch,} \hlkwc{col}\hlstd{=tmp}\hlopt{$}\hlstd{col)}
+\hlkwd{legend}\hlstd{(}\hlstr{"topright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"5 (score DGINN)"}\hlstd{,} \hlstr{"4"}\hlstd{,} \hlstr{"3"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/dotbats-1}
+
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tmp}\hlkwb{<-}\hlstd{maic[maic}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"gene"}\hlstd{,} \hlstr{"rank"}\hlstd{,} \hlstr{"nprimates"}\hlstd{)]}
+\hlstd{tmp}\hlkwb{<-}\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{decreasing} \hlstd{=} \hlnum{TRUE}\hlstd{),]}
+
+\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{5}\hlstd{]}\hlkwb{<-}\hlnum{1}
+\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlnum{20}
+\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{3}\hlstd{]}\hlkwb{<-}\hlnum{4}
+\hlstd{tmp}\hlopt{$}\hlstd{col}\hlkwb{<-}\hlstr{"black"}
+\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"ACE2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
+\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
+
+\hlkwd{dotchart}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{main}\hlstd{=}\hlstr{"Primates DGINN >=3"}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{labels}\hlstd{=tmp}\hlopt{$}\hlstd{gene,} \hlkwc{pch}\hlstd{=tmp}\hlopt{$}\hlstd{pch,} \hlkwc{cex}\hlstd{=}\hlnum{0.8}\hlstd{,} \hlkwc{col}\hlstd{=tmp}\hlopt{$}\hlstd{col)}
+\hlkwd{legend}\hlstd{(}\hlstr{"topright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"5 (score DGINN)"}\hlstd{,} \hlstr{"4"}\hlstd{,} \hlstr{"3"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/dotprimates-1}
+
+\end{knitrout}
+
+\section{Tanglegram}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{#install.packages('dendextend') # stable CRAN version}
+\hlkwd{library}\hlstd{(dendextend)} \hlcom{# load the package}
+\hlcom{#install.packages("phytools") # stable CRAN version}
+\hlkwd{library}\hlstd{(phytools)} \hlcom{# load the package}
+\hlkwd{library}\hlstd{(ggraph)}
+\hlkwd{library}\hlstd{(igraph)}
+\hlkwd{library}\hlstd{(tidyverse)}
+
+\hlcom{##}
+\hlstd{tmp}\hlkwb{<-}\hlstd{tablo[(tablo}\hlopt{$}\hlstd{nbats}\hlopt{!=}\hlnum{0} \hlopt{|} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{!=}\hlnum{0}\hlstd{),]}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{head}\hlstd{(tablo,} \hlnum{20}\hlstd{)}
+\hlcom{#tmp<-rbind(as.matrix(tmp), c("outgroup", 50, 50))}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp)}
+\hlstd{matbats}\hlkwb{<-}\hlkwd{hclust}\hlstd{(}\hlkwd{dist}\hlstd{(tmp}\hlopt{$}\hlstd{nbats))}
+\hlstd{matpri}\hlkwb{<-}\hlkwd{hclust}\hlstd{(}\hlkwd{dist}\hlstd{(tmp}\hlopt{$}\hlstd{nprimates))}
+
+
+\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{nbats),]}
+
+\hlstd{dendpri}\hlkwb{<-}\hlkwd{as.dendrogram}\hlstd{(matpri)}
+\hlstd{dendbats}\hlkwb{<-}\hlkwd{as.dendrogram}\hlstd{(matbats)}
+
+\hlkwd{labels}\hlstd{(dendpri)}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tmp}\hlopt{$}\hlstd{`tmp$Gene.name`[}\hlkwd{labels}\hlstd{(dendpri)])}
+\hlkwd{labels}\hlstd{(dendbats)}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tmp}\hlopt{$}\hlstd{`tmp$Gene.name`[}\hlkwd{labels}\hlstd{(dendbats)])}
+
+
+\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{nprimates,} \hlkwc{decreasing}\hlstd{=}\hlnum{FALSE}\hlstd{),]}\hlopt{$}\hlstr{'tmp$Gene.name'}\hlkwb{->} \hlstd{order}
+\hlstd{dendpri}\hlkwb{<-}\hlstd{dendextend}\hlopt{::}\hlkwd{rotate}\hlstd{(dendpri,} \hlkwc{order}\hlstd{=order)}
+
+\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{nbats,} \hlkwc{decreasing}\hlstd{=}\hlnum{FALSE}\hlstd{),]}\hlopt{$}\hlstr{'tmp$Gene.name'}\hlkwb{->} \hlstd{order}
+\hlstd{dendbats}\hlkwb{<-}\hlstd{dendextend}\hlopt{::}\hlkwd{rotate}\hlstd{(dendbats,} \hlkwc{order}\hlstd{=order)}
+
+\hlcom{#### Il faut swapper certains neuds de l'arbres}
+
+
+\hlkwd{class}\hlstd{(}\hlkwd{labels}\hlstd{(dendpri))}
+
+\hlstd{dend12} \hlkwb{<-} \hlkwd{dendlist}\hlstd{(dendbats, dendpri)}
+
+\hlopt{?}\hlstd{png}
+\hlkwd{png}\hlstd{(}\hlstr{"tanglegramm.png"}\hlstd{,} \hlkwc{width} \hlstd{=} \hlnum{1800}\hlstd{,} \hlkwc{height} \hlstd{=} \hlnum{3000}\hlstd{)}
+\hlkwd{tanglegram}\hlstd{(dend12,} \hlkwc{columns_width}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{3}\hlstd{,} \hlnum{3}\hlstd{,}\hlnum{3}\hlstd{),} \hlkwc{axes}\hlstd{=}\hlnum{FALSE}\hlstd{,}
+ \hlkwc{edge.lwd}\hlstd{=}\hlnum{0}\hlstd{,} \hlkwc{margin_inner}\hlstd{=}\hlnum{6}\hlstd{,}
+ \hlkwc{margin_top}\hlstd{=}\hlnum{2}\hlstd{,}
+ \hlkwc{main_left}\hlstd{=}\hlstr{" bats"}\hlstd{,}
+ \hlkwc{main_right} \hlstd{=} \hlstr{"primates "}\hlstd{,}
+ \hlkwc{lwd}\hlstd{=}\hlnum{0.5}\hlstd{,}
+ \hlkwc{cex_main}\hlstd{=}\hlnum{1}\hlstd{,}
+ \hlkwc{lab.cex}\hlstd{=}\hlnum{1}\hlstd{,}
+ \hlkwc{k_labels}\hlstd{=}\hlnum{6}\hlstd{)}
+
+\hlkwd{dev.off}\hlstd{()}
+
+\hlstd{tmp}
+\hlopt{?}\hlstd{tanglegram}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\end{document}
+
+
+
+
diff --git a/figure/boxplot-1.pdf b/figure/boxplot-1.pdf
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