diff --git a/covid_comp.Rnw b/covid_comp.Rnw
index e6adc513b49389503ea12cf8458567696940352f..45b79b52eb0e969117740c3c76551538876761d7 100644
--- a/covid_comp.Rnw
+++ b/covid_comp.Rnw
@@ -341,6 +341,21 @@ n12, n23, n13, n123,
category=c("DGINN-Young-primate", "Young-primate", "Cooper-primate"))
@
+\subsection{Mondrian}
+
+<<mondrianprimates>>=
+
+library(Mondrian)
+
+monddata<-as.data.frame(tmp$Gene.name)
+monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)
+monddata$primates_young<-ifelse(tmp$pVal.M8vsM7<0.05, 1, 0)
+monddata$primates_cooper<-ifelse(tmp$cooper.primates.M7.M8_p_val<0.05, 1, 0)
+
+mondrian(monddata[,2:4])
+@
+
+
%\subsection{Comparaison des codons?}
%Subtable with lines with both methods showing positive selection.
@@ -405,9 +420,21 @@ listjoined<-mapply(c, listdginn, listjanet, SIMPLIFY=FALSE)
Lecture du tableau.
+<<readtab4test, eval=F>>=
+# Tableau tel qu'il est à cet étape du script, pour travailler sur l'ajout du nouveau tableau bats sans recommencer au début à chaque fois.
+tab<-read.delim("COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt",
+ header=TRUE, sep="\t")
+@
+
<<>>=
-dginnbats<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv",
+#dginnbatsold<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv",
+# fill=T, h=T)
+
+
+dginnbats<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/DGINN_202005281339summary_cleaned.tab",
fill=T, h=T)
+
+
dim(dginnbats)
names(dginnbats)
length(unique(dginnbats$Gene))
@@ -425,42 +452,9 @@ Merge tables:
<<bats>>=
-add_col<-function(dginnfile=dginnbats, method="PamlM1M2", prefixe="bats_"){
-
-tmp<-dginn[dginnfile$Method==method,
- c("Gene", "Omega", "PosSel", "PValue", "NbSites", "PSS")]
-
-names(tmp)<-c("cooper.batsGene", paste0(prefixe, "Omega_", method),
- paste0(prefixe, "PosSel_", method), paste0(prefixe, "PValue_", method),
- paste0(prefixe, "NbSites_", method), paste0(prefixe, "PSS_", method))
-
-tab<-merge(tab, tmp, by="cooper.batsGene", all.x=T)
-
-return(tab)
-}
-
-tab<-add_col(dginnfile=dginnbats, method="PamlM1M2", prefixe="bats_")
+names(dginnbats)<-c("File", "bats_Name", "cooper.batsGene", paste0("bats_", names(dginnbats)[-(1:3)]))
-tab<-add_col(dginnfile=dginnbats, method="PamlM7M8", prefixe="bats_")
-
-tab<-add_col(dginnfile=dginnbats, method="BppM1M2", prefixe="bats_")
-
-tab<-add_col(dginnfile=dginnbats, method="BppM7M8", prefixe="bats_")
-
-
-head(na.omit(tab[, c("cooper.batsGene", "cooper.batsAverage_dNdS","cooper.batsM7.M8_p_value", "bats_Omega_PamlM7M8","bats_PValue_PamlM7M8")]))
-
-# Manip pour la colonne BUSTED
-
-tmp<-dginn[dginn$Method=="BUSTED",c("Gene", "Omega", "PosSel", "PValue")]
-names(tmp)<-c("cooper.batsGene", "bats_Omega_BUSTED", "bats_PosSel_BUSTED", "bats_PValue_BUSTED")
-tab<-merge(tab, tmp, all.x=T, by="cooper.batsGene")
-
-tmp<-dginn[dginn$Method=="MEME",c("Gene", "NbSites", "PSS")]
-names(tmp)<-c("cooper.batsGene", "bats_NbSites_MEME", "bats_PSS_MEME")
-tab<-merge(tab, tmp, all.x=T, by="cooper.batsGene")
-
-dim(tab)
+tab<-merge(tab,dginnbats, by="cooper.batsGene", all.x=T)
@
@@ -470,22 +464,23 @@ dim(tab)
<<omegaM7M8bats>>=
-plot(tab$cooper.batsAverage_dNdS, tab$bats_Omega_PamlM7M8,
+plot(tab$cooper.batsAverage_dNdS, tab$bats_omegaM0codeml,
xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
@
\subsubsection{pvalues pour M7M8}
<<pvalM7M8bats>>=
+tab$bats_codemlM7M8.p.value<-as.numeric(as.character(tab$bats_codemlM7M8.p.value))
-plot(tab$cooper.batsM7.M8_p_value, tab$bats_PValue_PamlM7M8, pch=20,
+plot(tab$cooper.batsM7.M8_p_value, tab$bats_codemlM7M8.p.value, pch=20,
xlab="p-value Cooper-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
-points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_PValue_PamlM7M8<0.05],
- tab$bats_PValue_PamlM7M8[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_PValue_PamlM7M8<0.05],
+points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_codemlM7M8.p.value<0.05],
+ tab$bats_codemlM7M8.p.value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_codemlM7M8.p.value<0.05],
col="red", pch=20)
-points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_PValue_PamlM7M8>0.05],
- tab$bats_PValue_PamlM7M8[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_PValue_PamlM7M8>0.05],
+points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_codemlM7M8.p.value>0.05],
+ tab$bats_codemlM7M8.p.value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_codemlM7M8.p.value>0.05],
col="green", pch=20)
@@ -531,17 +526,17 @@ legend("topleft", c("<0.05 in Hawkins but >0.05 in Cooper",
<<pvalM7M8compautre>>=
-plot(tab$hawkins_Positive.Selection..M8vM8a.p.value, tab$bats_PValue_PamlM7M8,
+plot(tab$hawkins_Positive.Selection..M8vM8a.p.value, tab$bats_codemlM7M8.p.value,
pch=20, xlab="p-value hawkins-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
points(tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
- tab$bats_PValue_PamlM7M8<0.05],
- tab$bats_PValue_PamlM7M8[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
- tab$bats_PValue_PamlM7M8<0.05], col="red", pch=20)
+ tab$bats_codemlM7M8.p.value<0.05],
+ tab$bats_codemlM7M8.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
+ tab$bats_codemlM7M8.p.value<0.05], col="red", pch=20)
points(tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
- tab$bats_PValue_PamlM7M8>0.05],
- tab$bats_PValue_PamlM7M8[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
- tab$bats_PValue_PamlM7M8>0.05], col="green", pch=20)
+ tab$bats_codemlM7M8.p.value>0.05],
+ tab$bats_codemlM7M8.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
+ tab$bats_codemlM7M8.p.value>0.05], col="green", pch=20)
legend("topleft", c("<0.05 in DGINN-bats but >0.05 in Hawkins",
@@ -561,7 +556,7 @@ I will draw a venn diagramm for the positive genes in the 3 analyses.
\subsubsection{subtab}
<<subbats>>=
-tmp<-na.omit(tab[,c("Gene.name", "bats_PValue_PamlM7M8", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value")])
+tmp<-na.omit(tab[,c("Gene.name", "bats_codemlM7M8.p.value", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value")])
dim(tmp)
@
@@ -569,24 +564,43 @@ dim(tmp)
\subsubsection{figure}
<<vennbats>>=
-area1dginn<-sum(tmp$bats_PValue_PamlM7M8<0.05, na.rm=T)
+area1dginn<-sum(tmp$bats_codemlM7M8.p.value<0.05, na.rm=T)
area2hawk<-sum(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
area3coop<-sum(tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
-n12<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
+n12<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
n23<-sum(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
-n13<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
+n13<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
+
+
+n123<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
+
+draw.triple.venn(area1dginn, area2hawk, area3coop,
+n12, n23, n13, n123,
+category=c("DGINN-Young-bats", "Hawkins-bats", "Cooper-bats"))
+
+@
-n123<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
+\subsection{Mondrian}
+<<mondrianbats>>=
+library(Mondrian)
-draw.triple.venn(area1dginn, area2hawk, area3coop, n12, n23, n13, n123, category=c("dginn", "hawkins", "cooper"))
+monddata<-as.data.frame(tmp$Gene.name)
+monddata$bats_dginn<-ifelse(tmp$bats_codemlM7M8.p.value<0.05, 1,0)
+monddata$bats_hawkins<-ifelse(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
+monddata$bats_cooper<-ifelse(tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
+
+mondrian(monddata[,2:4])
@
+\section{To do}
+
+Comparaison G4 pas G4
\end{document}
diff --git a/covid_comp.pdf b/covid_comp.pdf
index d025a82397e7d70eda322a967c96433034f800f6..e14d50ff9a0afb4c455f56c31d9313b987382db0 100644
Binary files a/covid_comp.pdf and b/covid_comp.pdf differ
diff --git a/covid_comp.tex b/covid_comp.tex
index c439678c8f36ec41627a190e565c8af10f29e3e2..1965f848b2bbb5177a80f8b362350f670b4f7e69 100644
--- a/covid_comp.tex
+++ b/covid_comp.tex
@@ -719,11 +719,31 @@ Il reste 186 gènes
\end{kframe}
\includegraphics[width=\maxwidth]{figure/vennprimate-1}
\begin{kframe}\begin{verbatim}
-## (polygon[GRID.polygon.497], polygon[GRID.polygon.498], polygon[GRID.polygon.499], polygon[GRID.polygon.500], polygon[GRID.polygon.501], polygon[GRID.polygon.502], text[GRID.text.503], text[GRID.text.504], text[GRID.text.505], text[GRID.text.506], text[GRID.text.507], text[GRID.text.508], text[GRID.text.509], text[GRID.text.510], text[GRID.text.511], text[GRID.text.512])
+## (polygon[GRID.polygon.836], polygon[GRID.polygon.837], polygon[GRID.polygon.838], polygon[GRID.polygon.839], polygon[GRID.polygon.840], polygon[GRID.polygon.841], text[GRID.text.842], text[GRID.text.843], text[GRID.text.844], text[GRID.text.845], text[GRID.text.846], text[GRID.text.847], text[GRID.text.848], text[GRID.text.849], text[GRID.text.850], text[GRID.text.851])
\end{verbatim}
\end{kframe}
\end{knitrout}
+\subsection{Mondrian}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(Mondrian)}
+
+\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+
+\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{])}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianprimates-1}
+
+\end{knitrout}
+
+
%\subsection{Comparaison des codons?}
%Subtable with lines with both methods showing positive selection.
@@ -757,25 +777,48 @@ Lecture du tableau.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv"}\hlstd{,}
+\hlcom{# Tableau tel qu'il est à cet étape du script, pour travailler sur l'ajout du nouveau tableau bats sans recommencer au début à chaque fois.}
+\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt"}\hlstd{,}
+ \hlkwc{header}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{#dginnbatsold<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv", }
+\hlcom{# fill=T, h=T)}
+
+
+\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/DGINN_202005281339summary_cleaned.tab"}\hlstd{,}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
+
+
\hlkwd{dim}\hlstd{(dginnbats)}
\end{alltt}
\begin{verbatim}
-## [1] 2904 9
+## [1] 349 27
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnbats)}
\end{alltt}
\begin{verbatim}
-## [1] "FullName" "Gene" "GeneSize" "Omega" "Method" "PosSel" "PValue"
-## [8] "NbSites" "PSS"
+## [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}
\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene))}
\end{alltt}
\begin{verbatim}
-## [1] 410
+## [1] 349
\end{verbatim}
\begin{alltt}
\hlkwd{length}\hlstd{(}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene))}
@@ -789,7 +832,7 @@ Lecture du tableau.
\begin{verbatim}
##
## FALSE TRUE
-## 4 214
+## 3 215
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -802,7 +845,7 @@ Which genes in the Cooper table are not in the gene output?
\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene)[}\hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsGene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F]}
\end{alltt}
\begin{verbatim}
-## [1] BCS1L C1orf50 CYB5B
+## [1] BCS1L C1orf50
## 218 Levels: AAR2 AASS AATF ACADM ACSL3 ADAMTS1 AGPS AKAP8L ALG11 ALG5 ... ZYG11B
\end{verbatim}
\end{kframe}
@@ -813,63 +856,10 @@ Merge 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{dginnfile}\hlstd{=dginnbats,} \hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{,} \hlkwc{prefixe}\hlstd{=}\hlstr{"bats_"}\hlstd{)\{}
-
-\hlstd{tmp}\hlkwb{<-}\hlstd{dginn[dginnfile}\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{"cooper.batsGene"}\hlstd{,} \hlkwd{paste0}\hlstd{(prefixe,} \hlstr{"Omega_"}\hlstd{, method),}
- \hlkwd{paste0}\hlstd{(prefixe,} \hlstr{"PosSel_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(prefixe,} \hlstr{"PValue_"}\hlstd{, method),}
- \hlkwd{paste0}\hlstd{(prefixe,} \hlstr{"NbSites_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(prefixe,} \hlstr{"PSS_"}\hlstd{, method))}
-
-\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
-
-\hlkwd{return}\hlstd{(tab)}
-\hlstd{\}}
-
-\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlkwc{dginnfile}\hlstd{=dginnbats,} \hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{,} \hlkwc{prefixe}\hlstd{=}\hlstr{"bats_"}\hlstd{)}
-
-\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlkwc{dginnfile}\hlstd{=dginnbats,} \hlkwc{method}\hlstd{=}\hlstr{"PamlM7M8"}\hlstd{,} \hlkwc{prefixe}\hlstd{=}\hlstr{"bats_"}\hlstd{)}
-
-\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlkwc{dginnfile}\hlstd{=dginnbats,} \hlkwc{method}\hlstd{=}\hlstr{"BppM1M2"}\hlstd{,} \hlkwc{prefixe}\hlstd{=}\hlstr{"bats_"}\hlstd{)}
+\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"cooper.batsGene"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"bats_"}\hlstd{,} \hlkwd{names}\hlstd{(dginnbats)[}\hlopt{-}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{)]))}
-\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlkwc{dginnfile}\hlstd{=dginnbats,} \hlkwc{method}\hlstd{=}\hlstr{"BppM7M8"}\hlstd{,} \hlkwc{prefixe}\hlstd{=}\hlstr{"bats_"}\hlstd{)}
-
-
-\hlkwd{head}\hlstd{(}\hlkwd{na.omit}\hlstd{(tab[,} \hlkwd{c}\hlstd{(}\hlstr{"cooper.batsGene"}\hlstd{,} \hlstr{"cooper.batsAverage_dNdS"}\hlstd{,}\hlstr{"cooper.batsM7.M8_p_value"}\hlstd{,} \hlstr{"bats_Omega_PamlM7M8"}\hlstd{,}\hlstr{"bats_PValue_PamlM7M8"}\hlstd{)]))}
-\end{alltt}
-\begin{verbatim}
-## cooper.batsGene cooper.batsAverage_dNdS cooper.batsM7.M8_p_value
-## 116 AAR2 0.12131411 0.99999000
-## 117 AASS 0.14147744 0.01076136
-## 118 AATF 0.12743890 0.78791584
-## 119 ACADM 0.17997029 0.00007550
-## 120 ACSL3 0.07628056 0.99994900
-## 121 ADAMTS1 0.08135086 0.76297348
-## bats_Omega_PamlM7M8 bats_PValue_PamlM7M8
-## 116 0.1367647 0.988919842
-## 117 0.1613940 0.073585521
-## 118 0.3249000 0.407786714
-## 119 0.3089985 0.003929791
-## 120 0.1038899 0.932307111
-## 121 0.1284746 0.999984000
-\end{verbatim}
-\begin{alltt}
-\hlcom{# Manip pour la colonne BUSTED}
-
-\hlstd{tmp}\hlkwb{<-}\hlstd{dginn[dginn}\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{"cooper.batsGene"}\hlstd{,} \hlstr{"bats_Omega_BUSTED"}\hlstd{,} \hlstr{"bats_PosSel_BUSTED"}\hlstd{,} \hlstr{"bats_PValue_BUSTED"}\hlstd{)}
-\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{all.x}\hlstd{=T,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{)}
-
-\hlstd{tmp}\hlkwb{<-}\hlstd{dginn[dginn}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"MEME"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}
-\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"cooper.batsGene"}\hlstd{,} \hlstr{"bats_NbSites_MEME"}\hlstd{,} \hlstr{"bats_PSS_MEME"}\hlstd{)}
-\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{all.x}\hlstd{=T,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{)}
-
-\hlkwd{dim}\hlstd{(tab)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
\end{alltt}
-\begin{verbatim}
-## [1] 332 134
-\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -881,7 +871,7 @@ Merge tables:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS, tab}\hlopt{$}\hlstd{bats_Omega_PamlM7M8,}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS, tab}\hlopt{$}\hlstd{bats_omegaM0codeml,}
\hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-bats"}\hlstd{)}
\end{alltt}
\end{kframe}
@@ -894,14 +884,19 @@ Merge tables:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value, tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
+\hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value))}
+\end{alltt}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value, tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
\hlkwc{xlab}\hlstd{=}\hlstr{"p-value Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
\hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
@@ -955,17 +950,17 @@ Merge tables:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value, tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8,}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value, tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value,}
\hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"p-value hawkins-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&}
- \hlstd{tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value[tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-bats but >0.05 in Hawkins"}\hlstd{,}
@@ -990,11 +985,11 @@ I will draw a venn diagramm for the positive genes in the 3 analyses.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_PValue_PamlM7M8"}\hlstd{,} \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,} \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{)])}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_codemlM7M8.p.value"}\hlstd{,} \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,} \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{)])}
\hlkwd{dim}\hlstd{(tmp)}
\end{alltt}
\begin{verbatim}
-## [1] 154 4
+## [1] 168 4
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -1005,31 +1000,54 @@ I will draw a venn diagramm for the positive genes in the 3 analyses.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlstd{area1dginn}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+\hlstd{area1dginn}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
\hlstd{area2hawk}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
\hlstd{area3coop}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-\hlstd{n12}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+\hlstd{n12}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
\hlstd{n23}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-\hlstd{n13}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+\hlstd{n13}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-\hlstd{n123}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+\hlstd{n123}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-
-\hlkwd{draw.triple.venn}\hlstd{(area1dginn, area2hawk, area3coop, n12, n23, n13, n123,} \hlkwc{category}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"dginn"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"cooper"}\hlstd{))}
+\hlkwd{draw.triple.venn}\hlstd{(area1dginn, area2hawk, area3coop,}
+\hlstd{n12, n23, n13, n123,}
+\hlkwc{category}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN-Young-bats"}\hlstd{,} \hlstr{"Hawkins-bats"}\hlstd{,} \hlstr{"Cooper-bats"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/vennbats-1}
\begin{kframe}\begin{verbatim}
-## (polygon[GRID.polygon.513], polygon[GRID.polygon.514], polygon[GRID.polygon.515], polygon[GRID.polygon.516], polygon[GRID.polygon.517], polygon[GRID.polygon.518], text[GRID.text.519], text[GRID.text.520], text[GRID.text.521], text[GRID.text.522], text[GRID.text.523], text[GRID.text.524], text[GRID.text.525], text[GRID.text.526], text[GRID.text.527], text[GRID.text.528])
+## (polygon[GRID.polygon.852], polygon[GRID.polygon.853], polygon[GRID.polygon.854], polygon[GRID.polygon.855], polygon[GRID.polygon.856], polygon[GRID.polygon.857], text[GRID.text.858], text[GRID.text.859], text[GRID.text.860], text[GRID.text.861], text[GRID.text.862], text[GRID.text.863], text[GRID.text.864], text[GRID.text.865], text[GRID.text.866], text[GRID.text.867])
\end{verbatim}
\end{kframe}
\end{knitrout}
+\subsection{Mondrian}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(Mondrian)}
+
+\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+
+\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{])}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/mondrianbats-1}
+
+\end{knitrout}
+
+\section{To do}
+
+Comparaison G4 pas G4
\end{document}
diff --git a/figure/mondrianbats-1.pdf b/figure/mondrianbats-1.pdf
new file mode 100644
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diff --git a/figure/omegaM7M8-1.pdf b/figure/omegaM7M8-1.pdf
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diff --git a/figure/omegaM7M8comp3-1.pdf b/figure/omegaM7M8comp3-1.pdf
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diff --git a/figure/pvalM7M8-1.pdf b/figure/pvalM7M8-1.pdf
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diff --git a/figure/pvalM7M8bats-1.pdf b/figure/pvalM7M8bats-1.pdf
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diff --git a/figure/pvalM7M8comp2-1.pdf b/figure/pvalM7M8comp2-1.pdf
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