diff --git a/covid_comp_primate-Young-focus.Rnw b/covid_comp_primate-Young-focus.Rnw
new file mode 100644
index 0000000000000000000000000000000000000000..292eac989936886689e2af264bae26b57b2b69a3
--- /dev/null
+++ b/covid_comp_primate-Young-focus.Rnw
@@ -0,0 +1,430 @@
+\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{October 2020} % Activate to display a given date or no date
+
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Files manipulations}
+
+\subsection{Read Janet Young's table}
+
+<<>>=
+workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
+
+tab<-read.delim(paste0(workdir,
+ "data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"),
+ fill=T, h=T, dec=",")
+dim(tab)
+
+#names(tab)
+
+@
+
+\subsection{Read DGINN Young table}
+
+DGINN-Young-primate table correspond to DGINN results, on the SAME alignment as Young-primate.
+
+I will merge the 2 tables.
+
+<<>>=
+dginnY<-read.delim(paste0(workdir,
+ "data/summary_primate_young.res"),
+ fill=T, h=T)
+
+dim(dginnY)
+
+names(dginnY)
+@
+
+
+\subsection{Joining Young and DGINN Young table}
+
+\textit{I hide some code corresponding to verifications of gene names coherence between tables}
+<<results="hide", echo=FALSE>>=
+head(tab)[,1:5]
+# gene avec un nom bizar dans certaines colomne
+tab[158,1:10]
+
+#
+length(unique(dginnY$Gene))
+length(unique(tab$PreyGene))
+length(unique(tab$Gene.name))
+
+#quelle paire de colonne contient le plus de noms identiques
+sum(unique(dginnY$Gene) %in% unique(tab$PreyGene))
+sum(unique(dginnY$Gene) %in% unique(tab$Gene.name))
+
+# dginn$Gene et tab$Gene.name presque identiques sauf 1 ligne.
+# Je soupçonne que c'est celle là :
+tab[158,1:10]
+
+# Verif:
+tab[,1:10][(tab$Gene.name %in% unique(dginnY$Gene))==F,]
+# yep
+
+# Remplacement manuel par
+as.character(unique(dginnY$Gene)[(unique(dginnY$Gene) %in% tab$Gene.name)==F])
+# dans le tableau de Janet
+
+val_remp=as.character(unique(dginnY$Gene)[(unique(dginnY$Gene) %in% tab$Gene.name)==F])
+
+tab$Gene.name<-as.character(tab$Gene.name)
+
+tab$Gene.name[158]<-val_remp
+
+sum(unique(dginnY$Gene) %in% unique(tab$Gene.name))
+@
+
+<<>>=
+
+add_col<-function(method="PamlM1M2"){
+
+tmp<-dginnY[dginnY$Method==method,
+ c("Gene", "Omega", "PosSel", "PValue", "NbSites", "PSS")]
+
+names(tmp)<-c("Gene.name", paste0("Omega_", method),
+ paste0("PosSel_", method), paste0("PValue_", method),
+ paste0("NbSites_", method), paste0("PSS_", method))
+
+tab<-merge(tab, tmp, by="Gene.name")
+
+return(tab)
+}
+
+tab<-add_col("PamlM1M2")
+tab<-add_col("PamlM7M8")
+tab<-add_col("BppM1M2")
+tab<-add_col("BppM7M8")
+
+
+# Manip pour la colonne BUSTED
+
+tmp<-dginnY[dginnY$Method=="BUSTED",c("Gene", "Omega", "PosSel", "PValue")]
+names(tmp)<-c("Gene.name", "Omega_BUSTED", "PosSel_BUSTED", "PValue_BUSTED")
+tab<-merge(tab, tmp, by="Gene.name")
+
+tmp<-dginnY[dginnY$Method=="MEME",c("Gene", "NbSites", "PSS")]
+names(tmp)<-c("Gene.name", "NbSites_MEME", "PSS_MEME")
+tab<-merge(tab, tmp, by="Gene.name")
+
+@
+
+
+\subsection{Read DGINN Table}
+
+<<>>=
+dginnT<-read.delim(paste0(workdir,
+"/data/DGINN_202005281649summary_cleaned.csv"),
+ fill=T, h=T, sep=",")
+
+dim(dginnT)
+
+names(dginnT)
+
+# Number of genes in dginn-primate output not present in the original table
+dginnT[(dginnT$Gene %in% tab$Gene.name)==F,"Gene"]
+# This includes paralogs, recombinations found by DGINN
+# and additionnal genes included on purpose
+
+# Number of genes from the original list not present in DGINN output
+tab[(tab$Gene.name %in% dginnT$Gene)==F,"Gene.name"]
+
+
+names(dginnT)<-c("File", "Name", "Gene.name", "GeneSize", "dginn-primate_NbSpecies", "dginn-primate_omegaM0Bpp",
+ "dginn-primate_omegaM0codeml", "dginn-primate_BUSTED", "dginn-primate_BUSTED.p.value",
+ "dginn-primate_MEME.NbSites", "dginn-primate_MEME.PSS", "dginn-primate_BppM1M2",
+ "dginn-primate_BppM1M2.p.value", "dginn-primate_BppM1M2.NbSites", "dginn-primate_BppM1M2.PSS",
+ "dginn-primate_BppM7M8", "dginn-primate_BppM7M8.p.value", "dginn-primate_BppM7M8.NbSites",
+ "dginn-primate_BppM7M8.PSS", "dginn-primate_codemlM1M2", "dginn-primate_codemlM1M2.p.value",
+ "dginn-primate_codemlM1M2.NbSites", "dginn-primate_codemlM1M2.PSS", "dginn-primate_codemlM7M8",
+ "dginn-primate_codemlM7M8.p.value", "dginn-primate_codemlM7M8.NbSites", "dginn-primate_codemlM7M8.PSS")
+
+@
+
+
+
+\subsection{Join Table and DGINN table}
+
+
+<<>>=
+tab<-merge(tab,dginnT, by="Gene.name", all.x=T)
+@
+
+
+\subsection{Write new table}
+<<>>=
+write.table(tab,
+ "COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20201014.txt",
+ row.names=F, quote=F, sep="\t")
+@
+
+
+
+
+
+
+
+
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Comparisons Primates}
+
+\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
+
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
+<<omegaM7M8>>=
+
+plot(tab$whole.gene.dN.dS.model.0, tab$Omega_PamlM7M8,
+ xlab="Omega Young-primate", ylab="Omega DGINN-Young-primate")
+abline(0,1)
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.2 & tab$Omega_PamlM7M8>0.4,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=(outlier$Omega_PamlM7M8+0.01),
+outlier$Gene.name)
+
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.6 & tab$Omega_PamlM7M8>0.7,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=(outlier$Omega_PamlM7M8+0.01),
+outlier$Gene.name)
+
+@
+
+
+
+\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS DGINN-full's results}
+
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
+<<omegaM7M8_2>>=
+
+tab$'dginn-primate_omegaM0Bpp'<-as.numeric(as.character(tab$'dginn-primate_omegaM0Bpp'))
+plot(tab$'dginn-primate_omegaM0Bpp', tab$Omega_PamlM7M8,
+ xlab="DGINN-full's", ylab="Omega DGINN-Young-primate")
+abline(0,1)
+
+outlier<-tab[tab$'dginn-primate_omegaM0Bpp'>0.4 & tab$Omega_PamlM7M8<0.2,]
+text(x=outlier$'dginn-primate_omegaM0Bpp',
+y=(outlier$Omega_PamlM7M8+0.01),
+outlier$Gene.name)
+
+outlier<-tab[tab$'dginn-primate_omegaM0Bpp'>0.5 & tab$Omega_PamlM7M8<0.4,]
+text(x=outlier$'dginn-primate_omegaM0Bpp',
+y=(outlier$Omega_PamlM7M8+0.01),
+outlier$Gene.name)
+
+@
+
+
+\subsection{Janet Young's results (Young-primate) VS DGINN-full's results}
+
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
+<<omegaM7M8_3>>=
+
+plot(tab$whole.gene.dN.dS.model.0, as.numeric(as.character(tab$'dginn-primate_omegaM0Bpp')),
+ xlab="Omega Young-primate", ylab="DGINN-full's")
+abline(0,1)
+
+
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 & tab$'dginn-primate_omegaM0Bpp'>0.5,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=outlier$'dginn-primate_omegaM0Bpp',
+outlier$Gene.name)
+
+@
+
+
+\section{Overlap}
+
+
+\subsection{Mondrian}
+
+<<mondrianprimates>>=
+
+library(Mondrian)
+
+#######
+
+monddata<-as.data.frame(tab$Gene.name)
+dim(monddata)
+
+dginnyoungtmp<-rowSums(cbind(tab$PosSel_PamlM1M2=="Y", tab$PosSel_PamlM7M8=="Y",
+tab$PosSel_BppM1M2=="Y", tab$PosSel_BppM7M8=="Y", tab$PosSel_BUSTED=="Y"))
+
+#monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)
+
+
+dginnfulltmp<-rowSums(cbind(tab$'dginn-primate_BUSTED'=="Y", tab$'dginn-primate_BppM1M2'=="Y",
+tab$'dginn-primate_BppM7M8'=="Y", tab$'dginn-primate_codemlM1M2'=="Y", tab$'dginn-primate_codemlM7M8'=="Y"))
+
+
+monddata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0)
+#monddata$primates_cooper<-ifelse(tab$cooper.primates.M7.M8_p_val<0.05, 1, 0)
+
+
+monddata$primates_dginn_young<-ifelse(dginnyoungtmp>=3, 1,0)
+monddata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
+
+mondrian(na.omit(monddata[,2:4]), labels=c("Young", "DGINN-Young >=3", "DGINN-full >=3" ))
+
+#####
+monddata$primates_dginn_young<-ifelse(dginnyoungtmp>=4, 1,0)
+monddata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0)
+
+mondrian(na.omit(monddata[,2:4]), labels=c("Young", "DGINN-Young >=4", "DGINN-full >=4"))
+@
+
+Comparison of results with the same method.
+<<>>=
+
+#####
+monddata$primates_dginn_young<-tab$PosSel_BppM7M8=="Y"
+monddata$primates_dginn_full<-tab$'dginn-primate_codemlM7M8'=="Y"
+
+mondrian(na.omit(monddata[,2:4]), labels=c("Young", "DGINN-Young", "DGINN-full"), main="posel codeml M7M8")
+@
+
+\subsection{subsetR}
+
+Just another representation of the same result.
+
+<<subsetprimates>>=
+library(UpSetR)
+upsetdata<-as.data.frame(tab$Gene.name)
+
+
+
+upsetdata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0)
+
+###
+upsetdata$primates_dginn_young<-ifelse(dginnyoungtmp>=3, 1,0)
+upsetdata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
+
+
+upset(na.omit(upsetdata), nsets = 3, matrix.color = "#DC267F",
+main.bar.color = "#648FFF", sets.bar.color = "#FE6100")
+
+###
+upsetdata$primates_dginn_young<-ifelse(dginnyoungtmp>=4, 1,0)
+upsetdata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0)
+
+upset(na.omit(upsetdata), nsets = 3, matrix.color = "#DC267F",
+main.bar.color = "#648FFF", sets.bar.color = "#FE6100")
+
+@
+
+\section{Gene List}
+
+Genes under positive selection for at least 4 methods.
+
+<<>>=
+dginnfulltmp<-rowSums(cbind(tab$'dginn-primate_BUSTED'=="Y",
+ tab$'dginn-primate_BppM1M2'=="Y",
+tab$'dginn-primate_BppM7M8'=="Y",
+tab$'dginn-primate_codemlM1M2'=="Y",
+tab$'dginn-primate_codemlM7M8'=="Y"))
+
+tab$Gene.name[dginnfulltmp>=4 & is.na(dginnfulltmp)==F]
+
+tab$Gene.name[dginnfulltmp>=3 & is.na(dginnfulltmp)==F]
+
+tmp<-tab[dginnfulltmp>=4 & is.na(dginnfulltmp)==F,
+c("Gene.name","dginn-primate_BUSTED", "dginn-primate_BppM1M2",
+ "dginn-primate_BppM7M8","dginn-primate_codemlM1M2","dginn-primate_codemlM7M8")]
+
+write.table(tmp, "geneList_DGINN_full_primate_pos4.txt", row.names=F, quote=F)
+@
+
+
+\section{Shiny like}
+
+<<shiny, fig.height=11>>=
+makeFig1 <- function(df){
+
+ # prepare data for colors etc
+ colMethods <- c("deepskyblue4", "darkorange" , "deepskyblue3" , "mediumseagreen" , "yellow3" , "black")
+ nameMethods <- c("BUSTED", "BppM1M2", "BppM7M8", "codemlM1M2", "codemlM7M8", "MEME")
+ metColor <- data.frame(Name = nameMethods , Col = colMethods , stringsAsFactors = FALSE)
+
+ # subset for this specific figure
+ #df <- df[df$nbY >= 1, ] # to drop genes found by 0 methods (big datasets)
+ xt <- df[, c("BUSTED", "BppM1M2", "BppM7M8", "codemlM1M2", "codemlM7M8")]
+ xt$Gene <- df$Gene
+ nbrMeth <- 5
+ # reverse order of dataframe so that genes with the most Y are at the bottom (to be on top of the barplot)
+ xt[,1:5] <- ifelse(xt[,1:5] == "Y", 1, 0)
+ # sort and Filter the 0 lines
+ xt<-xt[order(rowSums(xt[,1:5])),]
+ xt<-xt[rowSums(xt[,1:5])>2,]
+
+ row.names(xt)<-xt$Gene
+ xt<-xt[,1:5]
+
+ colFig1 <- metColor[which(metColor$Name %in% colnames(xt)) , ]
+
+ ##### PART 1 : NUMBER OF METHODS
+ par(xpd = NA , mar=c(2,7,4,0) , oma = c(0,0,0,0) , mgp = c(3,0.3,0))
+
+ h = barplot(
+ t(xt),
+ border = NA ,
+ axes = F ,
+ col = adjustcolor(colFig1$Col, alpha.f = 1),
+ horiz = T ,
+ las = 2 ,
+ main = "Methods detecting positive selection" ,
+ cex.main = 0.85,
+ cex.names = min(50/nrow(xt), 1.5)
+ )
+
+ axis(3, line = 0, at = c(0:nbrMeth), label = c("0", rep("", nbrMeth -1), nbrMeth), tck = 0.02)
+
+ legend("bottomleft",
+ horiz = T,
+ border = colFig1$Col,
+ legend = colFig1$Name,
+ fill = colFig1$Col,
+ cex = 0.8,
+ bty = "n",
+ xpd = NA
+ )
+}
+
+
+df<-read.delim(paste0(workdir,
+"/data/DGINN_202005281649summary_cleaned.csv"),
+ fill=T, h=T, sep=",")
+
+
+makeFig1(df)
+
+@
+
+\end{document}
+
diff --git a/covid_comp_primate-Young-focus.pdf b/covid_comp_primate-Young-focus.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..197adf5bf916f5b5381275e17db2fd800375e4fb
Binary files /dev/null and b/covid_comp_primate-Young-focus.pdf differ
diff --git a/covid_comp_primate-Young-focus.tex b/covid_comp_primate-Young-focus.tex
new file mode 100644
index 0000000000000000000000000000000000000000..43d236b66babd03f5177233f04d75cf6b6c475ee
--- /dev/null
+++ b/covid_comp_primate-Young-focus.tex
@@ -0,0 +1,609 @@
+\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{October 2020} % Activate to display a given date or no date
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\begin{document}
+\maketitle
+
+\tableofcontents
+
+\newpage
+
+\section{Files manipulations}
+
+\subsection{Read Janet Young's table}
+
+\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{"data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{","}\hlstd{)}
+\hlkwd{dim}\hlstd{(tab)}
+\end{alltt}
+\begin{verbatim}
+## [1] 332 84
+\end{verbatim}
+\begin{alltt}
+\hlcom{#names(tab)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\subsection{Read DGINN Young table}
+
+DGINN-Young-primate table correspond to DGINN results, on the SAME alignment as Young-primate.
+
+I will merge the 2 tables.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnY}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"data/summary_primate_young.res"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
+
+\hlkwd{dim}\hlstd{(dginnY)}
+\end{alltt}
+\begin{verbatim}
+## [1] 1992 7
+\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnY)}
+\end{alltt}
+\begin{verbatim}
+## [1] "Gene" "Omega" "Method" "PosSel" "PValue" "NbSites" "PSS"
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+\subsection{Joining Young and DGINN Young table}
+
+\textit{I hide some code corresponding to verifications of gene names coherence between tables}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{)\{}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstd{method,}
+ \hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}
+
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"Omega_"}\hlstd{, method),}
+ \hlkwd{paste0}\hlstd{(}\hlstr{"PosSel_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PValue_"}\hlstd{, method),}
+ \hlkwd{paste0}\hlstd{(}\hlstr{"NbSites_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PSS_"}\hlstd{, method))}
+
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
+
+\hlkwd{return}\hlstd{(tab)}
+\hlstd{\}}
+
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM1M2"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM7M8"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM1M2"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM7M8"}\hlstd{)}
+
+
+\hlcom{# Manip pour la colonne BUSTED}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"BUSTED"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{)]}
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"Omega_BUSTED"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{,} \hlstr{"PValue_BUSTED"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"MEME"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}
+\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"NbSites_MEME"}\hlstd{,} \hlstr{"PSS_MEME"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\subsection{Read DGINN Table}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+\hlstr{"/data/DGINN_202005281649summary_cleaned.csv"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
+
+\hlkwd{dim}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}
+## [1] 412 27
+\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnT)}
+\end{alltt}
+\begin{verbatim}
+## [1] "File" "Name" "Gene"
+## [4] "GeneSize" "NbSpecies" "omegaM0Bpp"
+## [7] "omegaM0codeml" "BUSTED" "BUSTED.p.value"
+## [10] "MEME.NbSites" "MEME.PSS" "BppM1M2"
+## [13] "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
+## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites"
+## [19] "BppM7M8.PSS" "codemlM1M2" "codemlM1M2.p.value"
+## [22] "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8"
+## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Number of genes in dginn-primate output not present in the original table}
+\hlstd{dginnT[(dginnT}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F,}\hlstr{"Gene"}\hlstd{]}
+\end{alltt}
+\begin{verbatim}
+## [1] ACE2 ADAM9[0-3120] ADAM9[3119-3927] ATP5MGL
+## [5] C1H1ORF50 CEP135[0-3264] CEP135[3263-3678] CEP43
+## [9] COQ8B COQ8A CSNK2A1 CSNK2B[0-609]
+## [13] CSNK2B[608-2568] CYB5R1 DDX21[0-717] DDX21[716-2538]
+## [17] DDX50 DNAJC15 DPH5[0-702] DPH5[701-1326]
+## [21] DPY19L2 ELOC ERO1B EXOSC3[0-1446]
+## [25] EXOSC3[1445-1980] FBN3 GNB4 GNB2
+## [29] GNB3 GOLGA7[0-312] GOLGA7[311-549] GPX1[0-1218]
+## [33] GPX1[1217-2946] HDAC1 HS6ST3 IMPDH1
+## [37] ITGB1[0-2328] ITGB1[2327-2844] LMAN2L MRPS5[0-1569]
+## [41] MRPS5[1568-3783] MARC2 MGRN1 NDFIP2[0-768]
+## [45] NDFIP2[767-1314] NDUFAF2[0-258] NDUFAF2[257-744] NSD2
+## [49] NUP58 NUP58[0-1824] NUP58[1823-2367] PABPC3
+## [53] POTPABPC1 PABPC4L PABPC5 PCSK5
+## [57] PRIM2[0-1071] PRIM2[1070-1902] PRKACB PRKACG
+## [61] PTGES2[0-1587] PTGES2[1586-2202] RAB8B RAB13
+## [65] RAB18[0-855] RAB18[854-1815] RAB2B RAB5A
+## [69] RAB5B RAB15 RALB EZR
+## [73] EZR[0-1458] EZR[1457-3771] MSN RETREG3
+## [77] RHOB RHOC SLC44A2[0-2577] SLC44A2[2576-3657]
+## [81] SPART SRP72[0-2604] SRP72[2603-3417] STOM[0-1047]
+## [85] STOM[1046-1800] STOML3 TIMM29 TLE4
+## [89] TLE2 TLE2[0-1302] TLE2[1301-3987] TMPRSS2
+## [93] TOMM70 TOR1B WASHC4 WFS1[0-2346]
+## [97] WFS1[2345-3216] YIF1B
+## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ... ZYG11B
+\end{verbatim}
+\begin{alltt}
+\hlcom{# This includes paralogs, recombinations found by DGINN }
+\hlcom{# and additionnal genes included on purpose}
+
+\hlcom{# Number of genes from the original list not present in DGINN output}
+\hlstd{tab[(tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F,}\hlstr{"Gene.name"}\hlstd{]}
+\end{alltt}
+\begin{verbatim}
+## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB"
+## [7] "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1" "SIGMAR1"
+## [13] "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP"
+## [19] "WHSC1"
+\end{verbatim}
+\begin{alltt}
+\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,} \hlstr{"dginn-primate_NbSpecies"}\hlstd{,} \hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{,}
+ \hlstr{"dginn-primate_omegaM0codeml"}\hlstd{,} \hlstr{"dginn-primate_BUSTED"}\hlstd{,} \hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{,}
+ \hlstr{"dginn-primate_MEME.NbSites"}\hlstd{,} \hlstr{"dginn-primate_MEME.PSS"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM7M8"}\hlstd{,} \hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{,}
+ \hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8"}\hlstd{,}
+ \hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
+\subsection{Join Table and DGINN table}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnT,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\subsection{Write new table}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{write.table}\hlstd{(tab,}
+ \hlstr{"COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20201014.txt"}\hlstd{,}
+ \hlkwc{row.names}\hlstd{=F,} \hlkwc{quote}\hlstd{=F,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
+
+
+
+
+
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Comparisons Primates}
+
+\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
+
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0, tab}\hlopt{$}\hlstd{Omega_PamlM7M8,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)}
+\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.2} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{>}\hlnum{0.4}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.6} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{>}\hlnum{0.7}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8-1}
+
+\end{knitrout}
+
+
+
+\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS DGINN-full's results}
+
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{, tab}\hlopt{$}\hlstd{Omega_PamlM7M8,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)}
+\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{<}\hlnum{0.2}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{,}
+\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.5} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{<}\hlnum{0.4}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{,}
+\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8_2-1}
+
+\end{knitrout}
+
+
+\subsection{Janet Young's results (Young-primate) VS DGINN-full's results}
+
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{)),}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{)}
+\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
+
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.5}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8_3-1}
+
+\end{knitrout}
+
+
+\section{Overlap}
+
+
+\subsection{Mondrian}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(Mondrian)}
+
+\hlcom{#######}
+
+\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
+\hlkwd{dim}\hlstd{(monddata)}
+\end{alltt}
+\begin{verbatim}
+## [1] 333 1
+\end{verbatim}
+\begin{alltt}
+\hlstd{dginnyoungtmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstd{PosSel_PamlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+\hlcom{#monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)}
+
+
+\hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_BUSTED'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn-primate_BppM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_BppM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn-primate_codemlM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn-primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+
+\hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlcom{#monddata$primates_cooper<-ifelse(tab$cooper.primates.M7.M8_p_val<0.05, 1, 0)}
+
+
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=3"}\hlstd{,} \hlstr{"DGINN-full >=3"} \hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianprimates-1}
+\begin{kframe}\begin{alltt}
+\hlcom{#####}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=4"}\hlstd{,} \hlstr{"DGINN-full >=4"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianprimates-2}
+
+\end{knitrout}
+
+Comparison of results with the same method.
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{#####}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}
+
+\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young"}\hlstd{,} \hlstr{"DGINN-full"}\hlstd{),} \hlkwc{main}\hlstd{=}\hlstr{"posel codeml M7M8"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/unnamed-chunk-8-1}
+
+\end{knitrout}
+
+\subsection{subsetR}
+
+Just another representation of the same result.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(UpSetR)}
+\hlstd{upsetdata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
+
+
+
+\hlstd{upsetdata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+
+\hlcom{###}
+\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+
+\hlkwd{upset}\hlstd{(}\hlkwd{na.omit}\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/subsetprimates-1}
+\begin{kframe}\begin{alltt}
+\hlcom{###}
+\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+\hlkwd{upset}\hlstd{(}\hlkwd{na.omit}\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/subsetprimates-2}
+
+\end{knitrout}
+
+\section{Gene List}
+
+Genes under positive selection for at least 4 methods.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_BUSTED'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+ \hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_BppM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_BppM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_codemlM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
+\end{alltt}
+\begin{verbatim}
+## [1] "ACADM" "BCS1L" "BRD4" "CDK5RAP2" "CEP135" "CEP68"
+## [7] "CLIP4" "DNMT1" "DPH5" "EMC1" "FYCO1" "GCC2"
+## [13] "GGH" "GHITM" "GIGYF2" "GLA" "GOLGA7" "HECTD1"
+## [19] "IDE" "ITGB1" "LARP1" "LARP4B" "LMAN2" "MARK1"
+## [25] "MIPOL1" "MPHOSPH10" "MYCBP2" "NDUFAF2" "NDUFB9" "PCNT"
+## [31] "POLA1" "PRIM2" "PRKAR2A" "PVR" "REEP6" "RIPK1"
+## [37] "SAAL1" "SEPSECS" "SIRT5" "SLC25A21" "SLC27A2" "TMEM39B"
+## [43] "TOR1AIP1" "TUBGCP2" "UBAP2" "UGGT2" "VPS39" "ZNF318"
+\end{verbatim}
+\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{3} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
+\end{alltt}
+\begin{verbatim}
+## [1] "ACADM" "ADAM9" "AP2A2" "ATE1" "BCS1L" "BRD4"
+## [7] "BZW2" "CDK5RAP2" "CEP135" "CEP68" "CLIP4" "CNTRL"
+## [13] "DNMT1" "DPH5" "EDEM3" "EIF4E2" "EMC1" "EXOSC2"
+## [19] "FYCO1" "GCC2" "GGH" "GHITM" "GIGYF2" "GLA"
+## [25] "GOLGA7" "GOLGB1" "GORASP1" "HDAC2" "HECTD1" "HS6ST2"
+## [31] "IDE" "ITGB1" "LARP1" "LARP4B" "LARP7" "LMAN2"
+## [37] "MARK1" "MDN1" "MIPOL1" "MOV10" "MPHOSPH10" "MRPS5"
+## [43] "MYCBP2" "NAT14" "NDUFAF2" "NDUFB9" "NGLY1" "NPC2"
+## [49] "PCNT" "PITRM1" "PLAT" "PLOD2" "PMPCB" "POLA1"
+## [55] "POR" "PRIM2" "PRKAR2A" "PTBP2" "PVR" "RAB14"
+## [61] "RAB1A" "RAB2A" "RAP1GDS1" "RBX1" "REEP6" "RIPK1"
+## [67] "RPL36" "SAAL1" "SCCPDH" "SEPSECS" "SIRT5" "SLC25A21"
+## [73] "SLC27A2" "STOM" "TIMM8B" "TMEM39B" "TOR1AIP1" "TRIM59"
+## [79] "TRMT1" "TUBGCP2" "UBAP2" "UGGT2" "USP54" "VPS39"
+## [85] "ZNF318"
+\end{verbatim}
+\begin{alltt}
+\hlstd{tmp}\hlkwb{<-}\hlstd{tab[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F,}
+\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,}\hlstr{"dginn-primate_BUSTED"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2"}\hlstd{,}
+ \hlstr{"dginn-primate_BppM7M8"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8"}\hlstd{)]}
+
+\hlkwd{write.table}\hlstd{(tmp,} \hlstr{"geneList_DGINN_full_primate_pos4.txt"}\hlstd{,} \hlkwc{row.names}\hlstd{=F,} \hlkwc{quote}\hlstd{=F)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+\section{Shiny like}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{makeFig1} \hlkwb{<-} \hlkwa{function}\hlstd{(}\hlkwc{df}\hlstd{)\{}
+
+ \hlcom{# prepare data for colors etc}
+ \hlstd{colMethods} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"deepskyblue4"}\hlstd{,} \hlstr{"darkorange"} \hlstd{,} \hlstr{"deepskyblue3"} \hlstd{,} \hlstr{"mediumseagreen"} \hlstd{,} \hlstr{"yellow3"} \hlstd{,} \hlstr{"black"}\hlstd{)}
+ \hlstd{nameMethods} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"BUSTED"}\hlstd{,} \hlstr{"BppM1M2"}\hlstd{,} \hlstr{"BppM7M8"}\hlstd{,} \hlstr{"codemlM1M2"}\hlstd{,} \hlstr{"codemlM7M8"}\hlstd{,} \hlstr{"MEME"}\hlstd{)}
+ \hlstd{metColor} \hlkwb{<-} \hlkwd{data.frame}\hlstd{(}\hlkwc{Name} \hlstd{= nameMethods ,} \hlkwc{Col} \hlstd{= colMethods ,} \hlkwc{stringsAsFactors} \hlstd{=} \hlnum{FALSE}\hlstd{)}
+
+ \hlcom{# subset for this specific figure}
+ \hlcom{#df <- df[df$nbY >= 1, ] # to drop genes found by 0 methods (big datasets)}
+ \hlstd{xt} \hlkwb{<-} \hlstd{df[,} \hlkwd{c}\hlstd{(}\hlstr{"BUSTED"}\hlstd{,} \hlstr{"BppM1M2"}\hlstd{,} \hlstr{"BppM7M8"}\hlstd{,} \hlstr{"codemlM1M2"}\hlstd{,} \hlstr{"codemlM7M8"}\hlstd{)]}
+ \hlstd{xt}\hlopt{$}\hlstd{Gene} \hlkwb{<-} \hlstd{df}\hlopt{$}\hlstd{Gene}
+ \hlstd{nbrMeth} \hlkwb{<-} \hlnum{5}
+ \hlcom{# reverse order of dataframe so that genes with the most Y are at the bottom (to be on top of the barplot)}
+ \hlstd{xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]} \hlkwb{<-} \hlkwd{ifelse}\hlstd{(xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]} \hlopt{==} \hlstr{"Y"}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+ \hlcom{# sort and Filter the 0 lines}
+ \hlstd{xt}\hlkwb{<-}\hlstd{xt[}\hlkwd{order}\hlstd{(}\hlkwd{rowSums}\hlstd{(xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{])),]}
+ \hlstd{xt}\hlkwb{<-}\hlstd{xt[}\hlkwd{rowSums}\hlstd{(xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{])}\hlopt{>}\hlnum{2}\hlstd{,]}
+
+ \hlkwd{row.names}\hlstd{(xt)}\hlkwb{<-}\hlstd{xt}\hlopt{$}\hlstd{Gene}
+ \hlstd{xt}\hlkwb{<-}\hlstd{xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]}
+
+ \hlstd{colFig1} \hlkwb{<-} \hlstd{metColor[}\hlkwd{which}\hlstd{(metColor}\hlopt{$}\hlstd{Name} \hlopt{%in%} \hlkwd{colnames}\hlstd{(xt)) , ]}
+
+ \hlcom{##### PART 1 : NUMBER OF METHODS}
+ \hlkwd{par}\hlstd{(}\hlkwc{xpd} \hlstd{=} \hlnum{NA} \hlstd{,} \hlkwc{mar}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{2}\hlstd{,}\hlnum{7}\hlstd{,}\hlnum{4}\hlstd{,}\hlnum{0}\hlstd{) ,} \hlkwc{oma} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{) ,} \hlkwc{mgp} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{3}\hlstd{,}\hlnum{0.3}\hlstd{,}\hlnum{0}\hlstd{))}
+
+ \hlstd{h} \hlkwb{=} \hlkwd{barplot}\hlstd{(}
+ \hlkwd{t}\hlstd{(xt),}
+ \hlkwc{border} \hlstd{=} \hlnum{NA} \hlstd{,}
+ \hlkwc{axes} \hlstd{= F ,}
+ \hlkwc{col} \hlstd{=} \hlkwd{adjustcolor}\hlstd{(colFig1}\hlopt{$}\hlstd{Col,} \hlkwc{alpha.f} \hlstd{=} \hlnum{1}\hlstd{),}
+ \hlkwc{horiz} \hlstd{= T ,}
+ \hlkwc{las} \hlstd{=} \hlnum{2} \hlstd{,}
+ \hlkwc{main} \hlstd{=} \hlstr{"Methods detecting positive selection"} \hlstd{,}
+ \hlkwc{cex.main} \hlstd{=} \hlnum{0.85}\hlstd{,}
+ \hlkwc{cex.names} \hlstd{=} \hlkwd{min}\hlstd{(}\hlnum{50}\hlopt{/}\hlkwd{nrow}\hlstd{(xt),} \hlnum{1.5}\hlstd{)}
+ \hlstd{)}
+
+ \hlkwd{axis}\hlstd{(}\hlnum{3}\hlstd{,} \hlkwc{line} \hlstd{=} \hlnum{0}\hlstd{,} \hlkwc{at} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlopt{:}\hlstd{nbrMeth),} \hlkwc{label} \hlstd{=} \hlkwd{c}\hlstd{(}\hlstr{"0"}\hlstd{,} \hlkwd{rep}\hlstd{(}\hlstr{""}\hlstd{, nbrMeth} \hlopt{-}\hlnum{1}\hlstd{), nbrMeth),} \hlkwc{tck} \hlstd{=} \hlnum{0.02}\hlstd{)}
+
+ \hlkwd{legend}\hlstd{(}\hlstr{"bottomleft"}\hlstd{,}
+ \hlkwc{horiz} \hlstd{= T,}
+ \hlkwc{border} \hlstd{= colFig1}\hlopt{$}\hlstd{Col,}
+ \hlkwc{legend} \hlstd{= colFig1}\hlopt{$}\hlstd{Name,}
+ \hlkwc{fill} \hlstd{= colFig1}\hlopt{$}\hlstd{Col,}
+ \hlkwc{cex} \hlstd{=} \hlnum{0.8}\hlstd{,}
+ \hlkwc{bty} \hlstd{=} \hlstr{"n"}\hlstd{,}
+ \hlkwc{xpd} \hlstd{=} \hlnum{NA}
+ \hlstd{)}
+\hlstd{\}}
+
+
+\hlstd{df}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+\hlstr{"/data/DGINN_202005281649summary_cleaned.csv"}\hlstd{),}
+ \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
+
+
+\hlkwd{makeFig1}\hlstd{(df)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/shiny-1}
+
+\end{knitrout}
+
+\end{document}
+