diff --git a/covid_comp_bats.Rnw b/covid_comp_bats.Rnw
index 08b9a62f0420ef963e9a20d0bb3498e08f7d6d14..279c190894cf75ffb6be9da2fd1f69cb28da075e 100644
--- a/covid_comp_bats.Rnw
+++ b/covid_comp_bats.Rnw
@@ -34,6 +34,8 @@ 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)
+tab$Gene.name<-as.character(tab$Gene.name)
+tab$Gene.name[tab$PreyGene=="MTARC1"]<-"MTARC1"
@
\section{Comparison Bats}
@@ -45,6 +47,7 @@ dim(tab)
plot(tab$cooper.batsAverage_dNdS, as.numeric(as.character(tab$bats_omegaM0codeml)),
xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
abline(0,1)
+abline(lm(as.numeric(as.character(tab$bats_omegaM0codeml))~tab$cooper.batsAverage_dNdS), col="red")
@
\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
@@ -56,13 +59,13 @@ abline(0,1)
\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<-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))
+tmp$bats_codemlM7M8_p.value<-as.numeric(as.character(tmp$bats_codemlM7M8_p.value))
dim(tmp)
@
-174 genes (present in the 3 experiments)
+170 genes (present in the 3 experiments)
\subsection{Mondrian}
@@ -105,9 +108,37 @@ main.bar.color = "#648FFF", sets.bar.color = "#FE6100")
@
+<<>>=
+source("covid_comp_shiny.R")
+
+
+df<-read.delim(paste0(workdir,
+"/data/DGINN_202005281649summary_cleaned.csv"),
+ fill=T, h=T, sep=",")
+names(df)
+dftmp<-tab[,c("bats_File", "bats_Name", "Gene.name",
+ "bats_GeneSize", "bats_NbSpecies", "bats_omegaM0Bpp",
+ "bats_omegaM0codeml", "bats_BUSTED", "bats_BUSTED_p.value",
+ "bats_MEME_NbSites", "bats_MEME_PSS", "bats_BppM1M2",
+ "bats_BppM1M2_p.value", "bats_BppM1M2_NbSites", "bats_BppM1M2_PSS",
+ "bats_BppM7M8", "bats_BppM7M8_p.value", "bats_BppM7M8_NbSites",
+ "bats_BppM7M8_PSS", "bats_codemlM1M2", "bats_codemlM1M2_p.value",
+ "bats_codemlM1M2_NbSites","bats_codemlM1M2_PSS", "bats_codemlM7M8",
+ "bats_codemlM7M8_p.value", "bats_codemlM7M8_NbSites" , "bats_codemlM7M8_PSS")]
+
+names(dftmp)<-names(df)
+makeFig1(dftmp)
+
+@
\end{document}
+
+
+
+
+
+
diff --git a/covid_comp_bats.pdf b/covid_comp_bats.pdf
index 6a94749512a2dd3398e2d43fe5a4e2ae8ac14fd0..ccdf459f9ee0c1633b0d1494840891dec816e06b 100644
Binary files a/covid_comp_bats.pdf and b/covid_comp_bats.pdf differ
diff --git a/covid_comp_bats.tex b/covid_comp_bats.tex
index 1334ecaf9228485f664fcd2e54e7bc4385fa13c9..492243c8a5276216ead8510bb5045919d59f19a1 100644
--- a/covid_comp_bats.tex
+++ b/covid_comp_bats.tex
@@ -88,8 +88,12 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\begin{verbatim}
-## [1] 333 161
+## [1] 332 139
\end{verbatim}
+\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name[tab}\hlopt{$}\hlstd{PreyGene}\hlopt{==}\hlstr{"MTARC1"}\hlstd{]}\hlkwb{<-}\hlstr{"MTARC1"}
+\end{alltt}
\end{kframe}
\end{knitrout}
@@ -107,8 +111,11 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
{\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{)}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0codeml))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
\end{alltt}
-\end{kframe}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in eval(predvars, data, env): NAs introduits lors de la conversion automatique}}\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8bats-1}
\end{knitrout}
@@ -124,9 +131,9 @@ 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{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}\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))}
+\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}
@@ -134,12 +141,12 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwd{dim}\hlstd{(tmp)}
\end{alltt}
\begin{verbatim}
-## [1] 174 9
+## [1] 170 9
\end{verbatim}
\end{kframe}
\end{knitrout}
-174 genes (present in the 3 experiments)
+170 genes (present in the 3 experiments)
\subsection{Mondrian}
@@ -199,9 +206,55 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\end{knitrout}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{source}\hlstd{(}\hlstr{"covid_comp_shiny.R"}\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{names}\hlstd{(df)}
+\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}
+\hlstd{dftmp}\hlkwb{<-}\hlstd{tab[,}\hlkwd{c}\hlstd{(}\hlstr{"bats_File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,}
+ \hlstr{"bats_GeneSize"}\hlstd{,} \hlstr{"bats_NbSpecies"}\hlstd{,} \hlstr{"bats_omegaM0Bpp"}\hlstd{,}
+ \hlstr{"bats_omegaM0codeml"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,} \hlstr{"bats_BUSTED_p.value"}\hlstd{,}
+ \hlstr{"bats_MEME_NbSites"}\hlstd{,} \hlstr{"bats_MEME_PSS"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,}
+ \hlstr{"bats_BppM1M2_p.value"}\hlstd{,} \hlstr{"bats_BppM1M2_NbSites"}\hlstd{,} \hlstr{"bats_BppM1M2_PSS"}\hlstd{,}
+ \hlstr{"bats_BppM7M8"}\hlstd{,} \hlstr{"bats_BppM7M8_p.value"}\hlstd{,} \hlstr{"bats_BppM7M8_NbSites"}\hlstd{,}
+ \hlstr{"bats_BppM7M8_PSS"}\hlstd{,} \hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM1M2_p.value"}\hlstd{,}
+ \hlstr{"bats_codemlM1M2_NbSites"}\hlstd{,}\hlstr{"bats_codemlM1M2_PSS"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{,}
+ \hlstr{"bats_codemlM7M8_p.value"}\hlstd{,} \hlstr{"bats_codemlM7M8_NbSites"} \hlstd{,} \hlstr{"bats_codemlM7M8_PSS"}\hlstd{)]}
+
+\hlkwd{names}\hlstd{(dftmp)}\hlkwb{<-}\hlkwd{names}\hlstd{(df)}
+\hlkwd{makeFig1}\hlstd{(dftmp)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/unnamed-chunk-2-1}
+\end{knitrout}
\end{document}
+
+
+
+
+
+
diff --git a/covid_comp_primate.Rnw b/covid_comp_primate.Rnw
new file mode 100644
index 0000000000000000000000000000000000000000..d502adf3daecec1e63da7a98eacd83ceb4495e7f
--- /dev/null
+++ b/covid_comp_primate.Rnw
@@ -0,0 +1,265 @@
+\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{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)
+tab$Gene.name<-as.character(tab$Gene.name)
+tab$Gene.name[tab$PreyGene=="MTARC1"]<-"MTARC1"
+
+@
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Comparisons Primates}
+
+\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_1>>=
+
+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)
+abline(lm(as.numeric(as.character(tab$dginn.primate_omegaM0Bpp))~tab$whole.gene.dN.dS.model.0), col="red")
+
+
+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$Gene.name)
+
+@
+
+\subsection{Janet Young's results (Young-primate) VS Cooper's result}
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.primates.Average\_dNdS".
+<<omegaM7M8_2>>=
+
+plot(tab$whole.gene.dN.dS.model.0, as.numeric(as.character(tab$cooper.primates.Average_dNdS)),
+ xlab="Omega Young-primate", ylab="Omega Cooper-primate")
+abline(0,1)
+abline(lm(as.numeric(as.character(tab$cooper.primates.Average_dNdS))~tab$whole.gene.dN.dS.model.0), col="red")
+
+
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 & tab$cooper.primates.Average_dNdS>0.5,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=outlier$cooper.primates.Average_dNdS,
+outlier$Gene.name)
+
+@
+
+\subsection{Cooper's results (Cooper-primate) VS DGINN-full's results}
+
+Comparaison des Omega: colonne "cooper.primates.Average\_dNdS" VS colonne "omega" dans la sortie de dginn.
+<<omegaM7M8_3>>=
+
+plot(tab$cooper.primates.Average_dNd, as.numeric(as.character(tab$dginn.primate_omegaM0Bpp)),
+ xlab="Omega Cooper-primate", ylab="DGINN-full's")
+abline(0,1)
+abline(lm(as.numeric(as.character(tab$dginn.primate_omegaM0Bpp))~tab$cooper.primates.Average_dNd), col="red")
+
+outlier<-tab[tab$cooper.primates.Average_dNd<0.4 & tab$dginn.primate_omegaM0Bpp>0.5,]
+text(x=outlier$cooper.primates.Average_dNd,
+y=outlier$dginn.primate_omegaM0Bpp,
+outlier$Gene.name)
+
+@
+
+
+
+
+
+
+\section{Overlap}
+
+
+\subsection{Mondrian}
+
+<<mondrianprimates>>=
+
+library(Mondrian)
+
+#######
+
+monddata<-as.data.frame(tab$Gene.name)
+dim(monddata)
+
+
+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$pVal.M8vsM7<0.05, 1, 0)
+monddata$primate_cooper<-ifelse(tab$cooper.primates.M7.M8_p_value<0.05, 1, 0)
+monddata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
+
+mondrian(na.omit(monddata[,2:4]), labels=c("Young", "Cooper", "DGINN-full >=3" ))
+
+#####
+monddata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0)
+
+mondrian(na.omit(monddata[,2:4]), labels=c("Young", "Cooper", "DGINN-full >=4"))
+@
+
+
+\subsection{subsetR}
+
+Just another representation of the same result.
+
+<<subsetprimates>>=
+library(UpSetR)
+upsetdata<-as.data.frame(tab$Gene.name)
+
+upsetdata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0)
+upsetdata$primate_cooper<-ifelse(tab$cooper.primates.M7.M8_p_value<0.05, 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_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
+ )
+}
+@
+
+<<>>=
+source("covid_comp_shiny.R")
+
+
+df<-read.delim(paste0(workdir,
+"/data/DGINN_202005281649summary_cleaned.csv"),
+ fill=T, h=T, sep=",")
+
+names(df)
+dftmp<-tab[,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")]
+
+names(dftmp)<-names(df)
+makeFig1(dftmp)
+
+@
+
+\end{document}
+
diff --git a/covid_comp_primate.pdf b/covid_comp_primate.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..0840330fbd5d2c6fb016cec3aadd243fb8922118
Binary files /dev/null and b/covid_comp_primate.pdf differ
diff --git a/covid_comp_primate.tex b/covid_comp_primate.tex
new file mode 100644
index 0000000000000000000000000000000000000000..145593b25b82c3ee2d452c4438f9253dc1cc5cd8
--- /dev/null
+++ b/covid_comp_primate.tex
@@ -0,0 +1,434 @@
+\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{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] 332 139
+\end{verbatim}
+\begin{alltt}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name[tab}\hlopt{$}\hlstd{PreyGene}\hlopt{==}\hlstr{"MTARC1"}\hlstd{]}\hlkwb{<-}\hlstr{"MTARC1"}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Comparisons Primates}
+
+\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{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp)),}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\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{)}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in eval(predvars, data, env): NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.5}\hlstd{,]}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in Ops.factor(tab\$dginn.primate\_omegaM0Bpp, 0.5): '>' not meaningful for factors}}\begin{alltt}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8_1-1}
+
+\end{knitrout}
+
+\subsection{Janet Young's results (Young-primate) VS Cooper's result}
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.primates.Average\_dNdS".
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS)),}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{)}
+\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS}\hlopt{>}\hlnum{0.5}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8_2-1}
+
+\end{knitrout}
+
+\subsection{Cooper's results (Cooper-primate) VS DGINN-full's results}
+
+Comparaison des Omega: colonne "cooper.primates.Average\_dNdS" 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{$}\hlstd{cooper.primates.Average_dNd,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp)),}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\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{)}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in eval(predvars, data, env): NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.5}\hlstd{,]}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in Ops.factor(tab\$dginn.primate\_omegaM0Bpp, 0.5): '>' not meaningful for factors}}\begin{alltt}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.primates.Average_dNd,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+\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] 332 1
+\end{verbatim}
+\begin{alltt}
+\hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{dginn.primate_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstd{dginn.primate_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{dginn.primate_codemlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{dginn.primate_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+\hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{primate_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\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{"Cooper"}\hlstd{,} \hlstr{"DGINN-full >=3"} \hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianprimates-1}
+\begin{kframe}\begin{alltt}
+\hlcom{#####}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+
+\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"Cooper"}\hlstd{,} \hlstr{"DGINN-full >=4"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianprimates-2}
+
+\end{knitrout}
+
+
+\subsection{subsetR}
+
+Just another representation of the same result.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(UpSetR)}
+\hlstd{upsetdata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\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{)}
+\hlstd{upsetdata}\hlopt{$}\hlstd{primate_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\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_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{$}\hlstd{dginn.primate_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstd{dginn.primate_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstd{dginn.primate_codemlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstd{dginn.primate_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+\hlstd{tab}\hlopt{$}\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"
+## [6] "CEP68" "CLIP4" "DNMT1" "DPH5" "EMC1"
+## [11] "FYCO1" "GCC2" "GGH" "GHITM" "GIGYF2"
+## [16] "GLA" "GOLGA7" "HECTD1" "IDE" "ITGB1"
+## [21] "LARP1" "LARP4B" "LMAN2" "MARK1" "MIPOL1"
+## [26] "MPHOSPH10" "MYCBP2" "NDUFAF2" "NDUFB9" "PCNT"
+## [31] "POLA1" "PRIM2" "PRKAR2A" "PVR" "REEP6"
+## [36] "RIPK1" "SAAL1" "SEPSECS" "SIRT5" "SLC25A21"
+## [41] "SLC27A2" "TMEM39B" "TOR1AIP1" "TUBGCP2" "UBAP2"
+## [46] "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"
+## [6] "BRD4" "BZW2" "CDK5RAP2" "CEP135" "CEP68"
+## [11] "CLIP4" "CNTRL" "DNMT1" "DPH5" "EDEM3"
+## [16] "EIF4E2" "EMC1" "EXOSC2" "FYCO1" "GCC2"
+## [21] "GGH" "GHITM" "GIGYF2" "GLA" "GOLGA7"
+## [26] "GOLGB1" "GORASP1" "HDAC2" "HECTD1" "HS6ST2"
+## [31] "IDE" "ITGB1" "LARP1" "LARP4B" "LARP7"
+## [36] "LMAN2" "MARK1" "MDN1" "MIPOL1" "MOV10"
+## [41] "MPHOSPH10" "MRPS5" "MYCBP2" "NAT14" "NDUFAF2"
+## [46] "NDUFB9" "NGLY1" "NPC2" "PCNT" "PITRM1"
+## [51] "PLAT" "PLOD2" "PMPCB" "POLA1" "POR"
+## [56] "PRIM2" "PRKAR2A" "PTBP2" "PVR" "RAB14"
+## [61] "RAB1A" "RAB2A" "RAP1GDS1" "RBX1" "REEP6"
+## [66] "RIPK1" "RPL36" "SAAL1" "SCCPDH" "SEPSECS"
+## [71] "SIRT5" "SLC25A21" "SLC27A2" "STOM" "TIMM8B"
+## [76] "TMEM39B" "TOR1AIP1" "TRIM59" "TRMT1" "TUBGCP2"
+## [81] "UBAP2" "UGGT2" "USP54" "VPS39" "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{\}}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{source}\hlstd{(}\hlstr{"covid_comp_shiny.R"}\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{names}\hlstd{(df)}
+\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}
+\hlstd{dftmp}\hlkwb{<-}\hlstd{tab[,}\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{)]}
+
+\hlkwd{names}\hlstd{(dftmp)}\hlkwb{<-}\hlkwd{names}\hlstd{(df)}
+\hlkwd{makeFig1}\hlstd{(dftmp)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/unnamed-chunk-3-1}
+
+\end{knitrout}
+
+\end{document}
+
diff --git a/covid_comp_shiny.R b/covid_comp_shiny.R
new file mode 100644
index 0000000000000000000000000000000000000000..b7f220d73644e3ad095632d9c0f3d15b90b7eaad
--- /dev/null
+++ b/covid_comp_shiny.R
@@ -0,0 +1,56 @@
+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$Gene
+ nbrMeth <- 5
+ # reverse order of dataframe so that genes with the most Y are at the bottom (to be on top of the barplot)
+ xt[,1:5] <- ifelse(xt[,1:5] == "Y", 1, 0)
+ # sort and Filter the 0 lines
+ xt<-xt[order(rowSums(xt[,1:5])),]
+ xt<-na.omit(xt[rowSums(xt[,1:5])>2,])
+
+ row.names(xt)<-xt$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=",")
+
diff --git a/figure/mondrianbats-1.pdf b/figure/mondrianbats-1.pdf
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diff --git a/figure/unnamed-chunk-3-1.pdf b/figure/unnamed-chunk-3-1.pdf
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diff --git a/geneList_DGINN_full_primate_pos4.txt b/geneList_DGINN_full_primate_pos4.txt
index 2b5ab577c11307f6e6f67482a055e4d0bc9eddd3..b8f446a07c096524234e109f0be8b2d1d644e85d 100644
--- a/geneList_DGINN_full_primate_pos4.txt
+++ b/geneList_DGINN_full_primate_pos4.txt
@@ -1,4 +1,4 @@
-Gene.name dginn-primate_BUSTED dginn-primate_BppM1M2 dginn-primate_BppM7M8 dginn-primate_codemlM1M2 dginn-primate_codemlM7M8
+Gene.name dginn.primate_BUSTED dginn.primate_BppM1M2 dginn.primate_BppM7M8 dginn.primate_codemlM1M2 dginn.primate_codemlM7M8
ACADM Y Y Y Y Y
BCS1L Y N Y Y Y
BRD4 Y Y Y N Y
@@ -34,7 +34,7 @@ PRIM2 Y Y Y Y Y
PRKAR2A N Y Y Y Y
PVR Y Y Y Y Y
REEP6 Y Y Y Y Y
-RIPK1 Y N Y Y Y
+RIPK1 N Y Y Y Y
SAAL1 Y N Y Y Y
SEPSECS Y Y Y Y Y
SIRT5 N Y Y Y Y