diff --git a/covid_comp.Rnw b/covid_comp.Rnw
index 47afac6595ca584a31224849f8173bf6905529df..e6adc513b49389503ea12cf8458567696940352f 100644
--- a/covid_comp.Rnw
+++ b/covid_comp.Rnw
@@ -20,11 +20,15 @@
\begin{document}
\maketitle
+\tableofcontents
+
+\newpage
+
\section{Files manipulations}
-I will compare Jeanette results to DGINN results, on the SAME alignment.
+I will compare Janet Young's results to DGINN results, on the SAME alignment.
-\subsection{Read Jeanette table}
+\subsection{Read Janet Young's table}
<<>>=
tab<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv",
@@ -74,7 +78,7 @@ tab[,1:10][(tab$Gene.name %in% unique(dginn$Gene))==F,]
# Remplacement manuel par
as.character(unique(dginn$Gene)[(unique(dginn$Gene) %in% tab$Gene.name)==F])
-# dans le tableau de Jeanette
+# dans le tableau de Janet
val_remp=as.character(unique(dginn$Gene)[(unique(dginn$Gene) %in% tab$Gene.name)==F])
@@ -85,7 +89,7 @@ tab$Gene.name[158]<-val_remp
sum(unique(dginn$Gene) %in% unique(tab$Gene.name))
@
-\subsubsection{new columns}
+\subsubsection{New columns}
<<>>=
@@ -121,16 +125,18 @@ tab<-merge(tab, tmp, by="Gene.name")
@
-\subsubsection{Write new table}
+\subsection{Write new table}
<<>>=
write.table(tab,
"COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt",
row.names=F, quote=F, sep="\t")
@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Comparisons Primates}
-\subsection{Figure}
-
+\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
\subsubsection{Omega}
@@ -138,7 +144,7 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
<<omegaM7M8>>=
plot(tab$whole.gene.dN.dS.model.0, tab$Omega_PamlM7M8,
- xlab="Omega tabJeanette", ylab="Omega DGINN")
+ xlab="Omega Young-primate", ylab="Omega DGINN-Young-primate")
@
Quels sont les 2 gènes qui s'écartent de la bissectrice?
<<>>=
@@ -155,7 +161,7 @@ Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + lign
<<pvalM7M8>>=
plot(tab$pVal.M8vsM7, tab$PValue_PamlM7M8, pch=20,
- xlab="p-value tabJeanette", ylab="p-value DGINN", main="M7vM8 Paml")
+ xlab="p-value Young-primate", ylab="p-value DGINN-Young-primate", main="M7vM8 Paml")
points(tab$pVal.M8vsM7[tab$pVal.M8vsM7>0.05 & tab$PValue_PamlM7M8<0.05],
tab$PValue_PamlM7M8[tab$pVal.M8vsM7>0.05 & tab$PValue_PamlM7M8<0.05],
col="red", pch=20)
@@ -163,8 +169,8 @@ points(tab$pVal.M8vsM7[tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8>0.05],
tab$PValue_PamlM7M8[tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8>0.05],
col="green", pch=20)
-legend("topleft", c("<0.05 in PamlM7M8 but >0.05 in Jeanette M8vsM7",
- "<0.05 in Jeanette M8vsM7 but >0.05 in PamlM7M8"),
+legend("topleft", c("<0.05 in DGINN-Young-primate PamlM7M8 but >0.05 in Young M8vsM7",
+ "<0.05 in Young M8vsM7 but >0.05 in DGINN-Young-primate PamlM7M8"),
pch=20, col=c("red", "green"))
@
@@ -189,11 +195,10 @@ tab[tab$Gene.name=="CIT",1:20]
-\subsubsection{Concordance est méthodes}
+\subsubsection{Concordance des méthodes}
Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 méthodes en général?
-
<<stripchart>>=
nontab<-tab[tab$pVal.M8vsM7>=0.05,c("Gene.name","PosSel_PamlM1M2", "PosSel_PamlM7M8","PosSel_BppM1M2",
"PosSel_BppM7M8", "PosSel_BUSTED")]
@@ -209,18 +214,139 @@ oui<-apply(ouitab, 1, function(x) sum(x=="Y"))
stripchart(x=list(oui, non), method="jitter", jitter=0.2,
vertical=T, pch=20, cex=0.5,
- group.names=c("Yes Jeanette", "No Jeanette"),
+ group.names=c("Yes Young", "No Young"),
ylab="Nb YES from dginn")
@
+\subsection{Résultats Cooper-primate VS Young-primate}
+
+\subsubsection{How many genes in the Cooper-primate columns?}
+
+<<>>=
+# Temporary table with necessary columns
+
+tmp<-tab[,c("Gene.name", "whole.gene.dN.dS.model.0", "pVal.M8vsM7",
+"cooper.primates.Gene", "cooper.primates.Average_dNdS",
+"cooper.primates.M7.M8_p_value")]
+dim(tmp)
+
+# Lines with values in the cooper Gene names column
+dim(tmp[tmp$cooper.primates.Gene!="",])
-%\subsubsection{Comparaison des codons?}
+# Line with values (no NA) in the Cooper dNdS column
+sum(is.na(tmp$cooper.primates.Average_dNdS)==F)
+
+# Line with values (no NA) in the Cooper pvalue column
+sum(is.na(tmp$cooper.primates.M7.M8_p_value)==F)
+@
+
+\subsubsection{Omega}
+
+Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.primates.Average\_dNdS"
+
+<<omegaM7M8coop>>=
+plot(tab$whole.gene.dN.dS.model.0, tab$cooper.primates.Average_dNdS,
+ xlab="Omega Young-primate", ylab="Omega Cooper-primate")
+@
+
+\subsubsection{pvalues pour M7M8}
+
+Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne cooper.primates.M7.M8\_p\_value (p-value de l'analyse de Cooper).
+
+<<pvalM7M8coop>>=
+
+plot(tab$pVal.M8vsM7, tab$cooper.primates.M7.M8_p_value, pch=20,
+ xlab="p-value Young", ylab="p-value Cooper-primate", main="M7vM8 Paml-primate")
+
+points(tab$pVal.M8vsM7[tab$pVal.M8vsM7>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
+ tab$cooper.primates.M7.M8_p_value[tab$pVal.M8vsM7>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
+ col="red", pch=20)
+points(tab$pVal.M8vsM7[tab$pVal.M8vsM7<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
+ tab$cooper.primates.M7.M8_p_value[tab$pVal.M8vsM7<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
+ col="green", pch=20)
+
+legend("topleft", c("<0.05 in Cooper PamlM7M8 but >0.05 in Young M8vsM7",
+ "<0.05 in Young M8vsM7 but >0.05 in Cooper PamlM7M8"),
+ pch=20, col=c("red", "green"))
+
+@
+
+\subsection{Résultats DGINN sur alignement de Janet-Young (DGINN-Young-primate) VS Cooper-primates}
+
+\subsubsection{Omega}
+
+Comparaison des Omega: colonne colonne "cooper.primates.Average\_dNdS" VS omega de DGINN.
+
+<<omegaM7M8comp3>>=
+plot(tab$Omega_PamlM7M8, tab$cooper.primates.Average_dNdS,
+ xlab="Omega DGINN-Young-primate", ylab="Omega Cooper-primate")
+@
+
+\subsubsection{pvalues pour M7M8}
+
+Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + ligne "PamlM7M8", pour la sortie de dginn.
+
+<<pvalM7M8comp3>>=
+
+plot(tab$PValue_PamlM7M8, tab$cooper.primates.M7.M8_p_value, pch=20,
+ xlab="p-value DGINN-Young-primate", ylab="p-value Cooper-primate", main="M7vM8 Paml")
+
+points(tab$PValue_PamlM7M8[tab$PValue_PamlM7M8>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
+ tab$cooper.primates.M7.M8_p_value[tab$PValue_PamlM7M8>0.05 & tab$cooper.primates.M7.M8_p_value<0.05],
+ col="red", pch=20)
+points(tab$PValue_PamlM7M8[tab$PValue_PamlM7M8<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
+ tab$cooper.primates.M7.M8_p_value[tab$PValue_PamlM7M8<0.05 & tab$cooper.primates.M7.M8_p_value>0.05],
+ col="green", pch=20)
+
+legend("topleft", c("<0.05 in Cooper-primate PamlM7M8 but >0.05 in DGINN-Young-primate M8vsM7",
+ "<0.05 in DGINN-Young-primate M8vsM7 but >0.05 in Cooper-primate PamlM7M8"),
+ pch=20, col=c("red", "green"))
+
+@
+
+\subsection{Overlap}
+
+I will draw a venn diagramm for the positive genes in the 3 analyses.
+
+\subsubsection{Library and subtable}
+
+<<sub>>=
+library(VennDiagram)
+
+# keeps only genes analysed in all 3 experiments
+tmp<-na.omit(tab[,c("Gene.name", "pVal.M8vsM7", "cooper.primates.M7.M8_p_value",
+ "PosSel_PamlM7M8", "PValue_PamlM7M8")])
+dim(tmp)
+@
+
+Il reste 186 gènes
+
+<<vennprimate>>=
+area1dginn<-sum(tmp$PosSel_PamlM7M8=="Y")
+area2jean<-sum(tmp$pVal.M8vsM7<0.05)
+area3coop<-sum(tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
+
+
+n12<-sum(tmp$PosSel_PamlM7M8=="Y" & tmp$pVal.M8vsM7<0.05)
+n23<-sum(tmp$pVal.M8vsM7<0.05 & tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
+n13<-sum(tmp$PosSel_PamlM7M8=="Y" & tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
+
+n123<-sum(tmp$PosSel_PamlM7M8=="Y" & tmp$pVal.M8vsM7<0.05 &
+tmp$cooper.primates.M7.M8_p_val<0.05, na.rm=T)
+
+draw.triple.venn(area1dginn, area2jean, area3coop,
+n12, n23, n13, n123,
+category=c("DGINN-Young-primate", "Young-primate", "Cooper-primate"))
+@
+
+%\subsection{Comparaison des codons?}
%Subtable with lines with both methods showing positive selection.
<<eval=FALSE, echo=FALSE>>=
+%<<selec>>=
#cas ou selection + dans les 2 cas
sel<-na.omit(tab[(tab$pVal.M8vsM7<0.05 & tab$PValue_PamlM7M8<0.05),c("Gene.name", "pVal.M8vsM7", "PValue_PamlM7M8", "whole.gene.dN.dS.model.0", "Omega_PamlM7M8", "Number.of.codons.with.BEB....0.9", "Codons.under.positive.selection..BEB..0.9...alignment.position.", "NbSites_PamlM7M8","PSS_PamlM7M8")])
@@ -228,10 +354,10 @@ dim(sel)
head(sel)
@
-
<<nsites, eval=FALSE, echo=FALSE>>=
+%<<nsites>>=
plot(sel$Number.of.codons.with.BEB....0.9, sel$NbSites_PamlM7M8)
-# toujours plus de codon dans la version de jeanette
+# toujours plus de codon dans la version de janet Young
listdginn<-sapply(sel$PSS_PamlM7M8, function(x){
tmp<-strsplit(as.character(x), split=",")[[1]]
@@ -247,7 +373,7 @@ listjanet<-sapply(sel$Codons.under.positive.selection..BEB..0.9...alignment.posi
tmp<-strsplit(as.character(x), split=",")[[1]]
tmp2<-sapply(tmp, function(x) strsplit(as.character(x), split="_")[[1]][1])
tmp2<-unlist(tmp2)
- names(tmp2)<-rep("jeanette", length(tmp2))
+ names(tmp2)<-rep("young", length(tmp2))
return(unlist(tmp2))
})
@@ -259,11 +385,23 @@ listjoined<-mapply(c, listdginn, listjanet, SIMPLIFY=FALSE)
-\section{Bats DGINN vs Bats Cooper}
-\subsection{Read DGINN table, Bats}
+
+
+
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Bats Comparisons}
+
+\subsection{Add DGINN results for Bats}
Lecture du tableau.
@@ -277,25 +415,15 @@ length(unique(tab$cooper.batsGene))
table(unique(tab$cooper.batsGene) %in% unique(dginnbats$Gene))
@
-Quels sont les gènes du tableau Cooper qui ne sont pas dans la sortie de DGINN
+Which genes in the Cooper table are not in the gene output?
<<>>=
unique(tab$cooper.batsGene)[unique(tab$cooper.batsGene) %in% unique(dginnbats$Gene)==F]
@
-Fusionner les tableaux
-
-
-
-
-
-
-
-
-
+Merge tables:
-
-<<last>>=
+<<bats>>=
add_col<-function(dginnfile=dginnbats, method="PamlM1M2", prefixe="bats_"){
@@ -320,59 +448,144 @@ tab<-add_col(dginnfile=dginnbats, method="BppM1M2", prefixe="bats_")
tab<-add_col(dginnfile=dginnbats, method="BppM7M8", prefixe="bats_")
-head(tab[, c("cooper.batsGene", "cooper.batsAverage_dNdS","cooper.batsM7.M8_p_value", "bats_Omega_PamlM7M8","bats_PValue_PamlM7M8")])
+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$Method=="BUSTED",c("Gene", "Omega", "PosSel", "PValue")]
names(tmp)<-c("cooper.batsGene", "bats_Omega_BUSTED", "bats_PosSel_BUSTED", "bats_PValue_BUSTED")
-tab<-merge(tab, tmp, by="cooper.batsGene")
+tab<-merge(tab, tmp, all.x=T, by="cooper.batsGene")
tmp<-dginn[dginn$Method=="MEME",c("Gene", "NbSites", "PSS")]
names(tmp)<-c("cooper.batsGene", "bats_NbSites_MEME", "bats_PSS_MEME")
-tab<-merge(tab, tmp, by="cooper.batsGene")
+tab<-merge(tab, tmp, all.x=T, by="cooper.batsGene")
dim(tab)
@
-\subsection{Comparaisons et figures}
-Faire un sous tableau.
-<<fig>>=
-tabbats<-na.omit(tab[, c("cooper.batsGene", "cooper.batsAverage_dNdS","cooper.batsM7.M8_p_value", "bats_Omega_PamlM7M8","bats_PValue_PamlM7M8")])
-dim(tabbats)
-@
+\subsection{Cooper-bats results vs DGINN-bats results}
-Comparaison des Omega
+\subsubsection{Omega}
<<omegaM7M8bats>>=
plot(tab$cooper.batsAverage_dNdS, tab$bats_Omega_PamlM7M8,
- xlab="Omega Cooper", ylab="Omega DGINN")
+ xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
@
-pvalues pour M7M8
+\subsubsection{pvalues pour M7M8}
<<pvalM7M8bats>>=
plot(tab$cooper.batsM7.M8_p_value, tab$bats_PValue_PamlM7M8, pch=20,
- xlab="p-value tabJeanette", ylab="p-value DGINN", main="M7vM8 Paml")
+ 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],
col="red", pch=20)
- points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_PValue_PamlM7M8>0.05],
+points(tab$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$bats_PValue_PamlM7M8>0.05],
col="green", pch=20)
-legend("topleft", c("<0.05 in PamlM7M8 but >0.05 in Jeanette M8vsM7",
- "<0.05 in Jeanette M8vsM7 but >0.05 in PamlM7M8"),
+legend("topleft", c("<0.05 in DGINN-bats but >0.05 in Cooper-bats",
+ "<0.05 in Cooper-bats but >0.05 in DGINN-bats"),
+ pch=20, col=c("red", "green"))
+
+@
+
+
+
+
+\subsection{Comparaison Cooper-Hawkins}
+
+
+\subsubsection{pvalues pour M7M8}
+
+<<pvalM7M8comp2>>=
+
+plot(tab$cooper.batsM7.M8_p_value, tab$hawkins_Positive.Selection..M8vM8a.p.value,
+ pch=20, xlab="p-value Cooper-bats", ylab="p-value hawkins-bats", main="M7vM8 Paml")
+
+points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 &
+ tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05],
+ tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$cooper.batsM7.M8_p_value>0.05 &
+ tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05],
+ col="red", pch=20)
+points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 &
+ tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05],
+ tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$cooper.batsM7.M8_p_value<0.05 &
+ tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05],
+ col="green", pch=20)
+
+
+legend("topleft", c("<0.05 in Hawkins but >0.05 in Cooper",
+ "<0.05 in Cooper but >0.05 in Hawkins"),
+ pch=20, col=c("red", "green"))
+
+@
+
+
+\subsection{Comparaison dginn-Hawkins}
+
+<<pvalM7M8compautre>>=
+
+plot(tab$hawkins_Positive.Selection..M8vM8a.p.value, tab$bats_PValue_PamlM7M8,
+ pch=20, xlab="p-value hawkins-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
+
+points(tab$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$bats_PValue_PamlM7M8<0.05], col="red", pch=20)
+points(tab$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$bats_PValue_PamlM7M8>0.05], col="green", pch=20)
+
+
+legend("topleft", c("<0.05 in DGINN-bats but >0.05 in Hawkins",
+ "<0.05 in Hawkinsbut >0.05 in DGINN-bats"),
pch=20, col=c("red", "green"))
@
-Apparemment, ces comparaisons n'ont pas trop de sens.
+
+
+
+
+\subsection{Diagramme de Venn}
+
+I will draw a venn diagramm for the positive genes in the 3 analyses.
+
+\subsubsection{subtab}
+
+<<subbats>>=
+tmp<-na.omit(tab[,c("Gene.name", "bats_PValue_PamlM7M8", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value")])
+dim(tmp)
+@
+
+154 genes (present in the 3 experiments)
+
+\subsubsection{figure}
+<<vennbats>>=
+area1dginn<-sum(tmp$bats_PValue_PamlM7M8<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)
+
+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)
+
+
+n123<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
+
+
+draw.triple.venn(area1dginn, area2hawk, area3coop, n12, n23, n13, n123, category=c("dginn", "hawkins", "cooper"))
+@
\end{document}
diff --git a/covid_comp.pdf b/covid_comp.pdf
index 66726a7a5915ff26aa1127ea677b64553cc8a18f..d025a82397e7d70eda322a967c96433034f800f6 100644
Binary files a/covid_comp.pdf and b/covid_comp.pdf differ
diff --git a/covid_comp.tex b/covid_comp.tex
index 28d0f7ee75669c44e06bb28e2de3fb82987037c1..c439678c8f36ec41627a190e565c8af10f29e3e2 100644
--- a/covid_comp.tex
+++ b/covid_comp.tex
@@ -70,11 +70,15 @@
\begin{document}
\maketitle
+\tableofcontents
+
+\newpage
+
\section{Files manipulations}
-I will compare Jeanette results to DGINN results, on the SAME alignment.
+I will compare Janet Young's results to DGINN results, on the SAME alignment.
-\subsection{Read Jeanette table}
+\subsection{Read Janet Young's table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -297,7 +301,7 @@ I will compare Jeanette results to DGINN results, on the SAME alignment.
## [1] "MARC1"
\end{verbatim}
\begin{alltt}
-\hlcom{# dans le tableau de Jeanette}
+\hlcom{# dans le tableau de Janet}
\hlstd{val_remp}\hlkwb{=}\hlkwd{as.character}\hlstd{(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)[(}\hlkwd{unique}\hlstd{(dginn}\hlopt{$}\hlstd{Gene)} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F])}
@@ -313,7 +317,7 @@ I will compare Jeanette results to DGINN results, on the SAME alignment.
\end{kframe}
\end{knitrout}
-\subsubsection{new columns}
+\subsubsection{New columns}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -351,7 +355,7 @@ I will compare Jeanette results to DGINN results, on the SAME alignment.
\end{kframe}
\end{knitrout}
-\subsubsection{Write new table}
+\subsection{Write new table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
@@ -362,9 +366,11 @@ I will compare Jeanette results to DGINN results, on the SAME alignment.
\end{kframe}
\end{knitrout}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Comparisons Primates}
-\subsection{Figure}
-
+\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
\subsubsection{Omega}
@@ -373,7 +379,7 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
\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 tabJeanette"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN"}\hlstd{)}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8-1}
@@ -406,7 +412,7 @@ Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + lign
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7, tab}\hlopt{$}\hlstd{PValue_PamlM7M8,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"p-value tabJeanette"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-Young-primate"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
\hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],}
\hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
@@ -414,8 +420,8 @@ Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + lign
\hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\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 PamlM7M8 but >0.05 in Jeanette M8vsM7"}\hlstd{,}
- \hlstr{"<0.05 in Jeanette M8vsM7 but >0.05 in PamlM7M8"}\hlstd{),}
+\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-Young-primate PamlM7M8 but >0.05 in Young M8vsM7"}\hlstd{,}
+ \hlstr{"<0.05 in Young M8vsM7 but >0.05 in DGINN-Young-primate PamlM7M8"}\hlstd{),}
\hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
\end{alltt}
\end{kframe}
@@ -513,11 +519,10 @@ Focus sur le gène CIT pour lequel la différence est vraiment assez importante:
-\subsubsection{Concordance est méthodes}
+\subsubsection{Concordance des méthodes}
Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 méthodes en général?
-
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
@@ -535,7 +540,7 @@ Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 m
\hlkwd{stripchart}\hlstd{(}\hlkwc{x}\hlstd{=}\hlkwd{list}\hlstd{(oui, non),} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{jitter}\hlstd{=}\hlnum{0.2}\hlstd{,}
\hlkwc{vertical}\hlstd{=T,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{,}
- \hlkwc{group.names}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Yes Jeanette"}\hlstd{,} \hlstr{"No Jeanette"}\hlstd{),}
+ \hlkwc{group.names}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Yes Young"}\hlstd{,} \hlstr{"No Young"}\hlstd{),}
\hlkwc{ylab}\hlstd{=}\hlstr{"Nb YES from dginn"}\hlstd{)}
\end{alltt}
\end{kframe}
@@ -543,8 +548,183 @@ Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 m
\end{knitrout}
+\subsection{Résultats Cooper-primate VS Young-primate}
+
+\subsubsection{How many genes in the Cooper-primate columns?}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlcom{# Temporary table with necessary columns}
+
+\hlstd{tmp}\hlkwb{<-}\hlstd{tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"whole.gene.dN.dS.model.0"}\hlstd{,} \hlstr{"pVal.M8vsM7"}\hlstd{,}
+\hlstr{"cooper.primates.Gene"}\hlstd{,} \hlstr{"cooper.primates.Average_dNdS"}\hlstd{,}
+\hlstr{"cooper.primates.M7.M8_p_value"}\hlstd{)]}
+\hlkwd{dim}\hlstd{(tmp)}
+\end{alltt}
+\begin{verbatim}
+## [1] 332 6
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Lines with values in the cooper Gene names column}
+\hlkwd{dim}\hlstd{(tmp[tmp}\hlopt{$}\hlstd{cooper.primates.Gene}\hlopt{!=}\hlstr{""}\hlstd{,])}
+\end{alltt}
+\begin{verbatim}
+## [1] 207 6
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Line with values (no NA) in the Cooper dNdS column}
+\hlkwd{sum}\hlstd{(}\hlkwd{is.na}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.Average_dNdS)}\hlopt{==}\hlstd{F)}
+\end{alltt}
+\begin{verbatim}
+## [1] 201
+\end{verbatim}
+\begin{alltt}
+\hlcom{# Line with values (no NA) in the Cooper pvalue column}
+\hlkwd{sum}\hlstd{(}\hlkwd{is.na}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value)}\hlopt{==}\hlstd{F)}
+\end{alltt}
+\begin{verbatim}
+## [1] 207
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+\subsubsection{Omega}
+
+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{$}\hlstd{whole.gene.dN.dS.model.0, tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8coop-1}
+
+\end{knitrout}
+
+\subsubsection{pvalues pour M7M8}
+
+Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne cooper.primates.M7.M8\_p\_value (p-value de l'analyse de Cooper).
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7, tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Young"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value Cooper-primate"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml-primate"}\hlstd{)}
+
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{>}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_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 Cooper PamlM7M8 but >0.05 in Young M8vsM7"}\hlstd{,}
+ \hlstr{"<0.05 in Young M8vsM7 but >0.05 in Cooper PamlM7M8"}\hlstd{),}
+ \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/pvalM7M8coop-1}
+
+\end{knitrout}
+
+\subsection{Résultats DGINN sur alignement de Janet-Young (DGINN-Young-primate) VS Cooper-primates}
+
+\subsubsection{Omega}
+
+Comparaison des Omega: colonne colonne "cooper.primates.Average\_dNdS" VS omega de DGINN.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{Omega_PamlM7M8, tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/omegaM7M8comp3-1}
+
+\end{knitrout}
+
+\subsubsection{pvalues pour M7M8}
+
+Cette fois, je compare la colonne R "pVal.M8vsM7", Ã la colonne "PValue" + ligne "PamlM7M8", pour 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{$}\hlstd{PValue_PamlM7M8, tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"p-value DGINN-Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value Cooper-primate"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
+
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{>}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{PValue_PamlM7M8[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value}\hlopt{>}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_value[tab}\hlopt{$}\hlstd{PValue_PamlM7M8}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.M7.M8_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 Cooper-primate PamlM7M8 but >0.05 in DGINN-Young-primate M8vsM7"}\hlstd{,}
+ \hlstr{"<0.05 in DGINN-Young-primate M8vsM7 but >0.05 in Cooper-primate PamlM7M8"}\hlstd{),}
+ \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/pvalM7M8comp3-1}
+
+\end{knitrout}
+
+\subsection{Overlap}
+
+I will draw a venn diagramm for the positive genes in the 3 analyses.
+
+\subsubsection{Library and subtable}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{library}\hlstd{(VennDiagram)}
+
+\hlcom{# keeps only genes analysed in all 3 experiments}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"pVal.M8vsM7"}\hlstd{,} \hlstr{"cooper.primates.M7.M8_p_value"}\hlstd{,}
+ \hlstr{"PosSel_PamlM7M8"}\hlstd{,} \hlstr{"PValue_PamlM7M8"}\hlstd{)])}
+\hlkwd{dim}\hlstd{(tmp)}
+\end{alltt}
+\begin{verbatim}
+## [1] 186 5
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+Il reste 186 gènes
+
+\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{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{)}
+\hlstd{area2jean}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{)}
+\hlstd{area3coop}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+
+
+\hlstd{n12}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{)}
+\hlstd{n23}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+\hlstd{n13}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
-%\subsubsection{Comparaison des codons?}
+\hlstd{n123}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"} \hlopt{&} \hlstd{tmp}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05} \hlopt{&}
+\hlstd{tmp}\hlopt{$}\hlstd{cooper.primates.M7.M8_p_val}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+
+\hlkwd{draw.triple.venn}\hlstd{(area1dginn, area2jean, area3coop,}
+\hlstd{n12, n23, n13, n123,}
+\hlkwc{category}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN-Young-primate"}\hlstd{,} \hlstr{"Young-primate"}\hlstd{,} \hlstr{"Cooper-primate"}\hlstd{))}
+\end{alltt}
+\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])
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+%\subsection{Comparaison des codons?}
%Subtable with lines with both methods showing positive selection.
@@ -555,11 +735,22 @@ Est-ce que les gènes avec une faible p-value sont détecté par 1,2,3,4 ou 5 m
-\section{Bats DGINN vs Bats Cooper}
-\subsection{Read DGINN table, Bats}
+
+
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{Bats Comparisons}
+
+\subsection{Add DGINN results for Bats}
Lecture du tableau.
@@ -603,7 +794,7 @@ Lecture du tableau.
\end{kframe}
\end{knitrout}
-Quels sont les gènes du tableau Cooper qui ne sont pas dans la sortie de DGINN
+Which genes in the Cooper table are not in the gene output?
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -617,17 +808,7 @@ Quels sont les gènes du tableau Cooper qui ne sont pas dans la sortie de DGINN
\end{kframe}
\end{knitrout}
-Fusionner les tableaux
-
-
-
-
-
-
-
-
-
-
+Merge tables:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
@@ -655,89 +836,77 @@ Fusionner les tableaux
\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{(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{)])}
+\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
-## 1 NA NA
-## 2 NA NA
-## 3 NA NA
-## 4 NA NA
-## 5 NA NA
-## 6 NA NA
-## bats_Omega_PamlM7M8 bats_PValue_PamlM7M8
-## 1 NA NA
-## 2 NA NA
-## 3 NA NA
-## 4 NA NA
-## 5 NA NA
-## 6 NA NA
+## 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{$}\hlstd{Method}\hlopt{==}\hlstr{"BUSTED"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{)]}
\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"cooper.batsGene"}\hlstd{,} \hlstr{"bats_Omega_BUSTED"}\hlstd{,} \hlstr{"bats_PosSel_BUSTED"}\hlstd{,} \hlstr{"bats_PValue_BUSTED"}\hlstd{)}
-\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{)}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{all.x}\hlstd{=T,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{)}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginn[dginn}\hlopt{$}\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{by}\hlstd{=}\hlstr{"cooper.batsGene"}\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)}
\end{alltt}
\begin{verbatim}
-## [1] 211 134
+## [1] 332 134
\end{verbatim}
\end{kframe}
\end{knitrout}
-\subsection{Comparaisons et figures}
-Faire un sous tableau.
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{tabbats}\hlkwb{<-}\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{)])}
-\hlkwd{dim}\hlstd{(tabbats)}
-\end{alltt}
-\begin{verbatim}
-## [1] 189 5
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
+\subsection{Cooper-bats results vs DGINN-bats results}
-Comparaison des Omega
+\subsubsection{Omega}
\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,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN"}\hlstd{)}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-bats"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8bats-1}
\end{knitrout}
-pvalues pour M7M8
+\subsubsection{pvalues pour M7M8}
\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{,}
- \hlkwc{xlab}\hlstd{=}\hlstr{"p-value tabJeanette"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\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{],}
\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{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],}
\hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
-\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in PamlM7M8 but >0.05 in Jeanette M8vsM7"}\hlstd{,}
- \hlstr{"<0.05 in Jeanette M8vsM7 but >0.05 in PamlM7M8"}\hlstd{),}
+\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-bats but >0.05 in Cooper-bats"}\hlstd{,}
+ \hlstr{"<0.05 in Cooper-bats but >0.05 in DGINN-bats"}\hlstd{),}
\hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
\end{alltt}
\end{kframe}
@@ -745,7 +914,121 @@ pvalues pour M7M8
\end{knitrout}
-Apparemment, ces comparaisons n'ont pas trop de sens.
+
+
+
+\subsection{Comparaison Cooper-Hawkins}
+
+
+\subsubsection{pvalues pour M7M8}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value, tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value,}
+ \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"p-value Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value hawkins-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
+
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{>}\hlnum{0.05} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{],}
+ \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
+ \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value[tab}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{>}\hlnum{0.05}\hlstd{],}
+ \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+
+
+\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in Hawkins but >0.05 in Cooper"}\hlstd{,}
+ \hlstr{"<0.05 in Cooper but >0.05 in Hawkins"}\hlstd{),}
+ \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/pvalM7M8comp2-1}
+
+\end{knitrout}
+
+
+\subsection{Comparaison dginn-Hawkins}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value, tab}\hlopt{$}\hlstd{bats_PValue_PamlM7M8,}
+ \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"p-value hawkins-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"p-value DGINN-bats"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"M7vM8 Paml"}\hlstd{)}
+
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+\hlkwd{points}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{>}\hlnum{0.05}\hlstd{],} \hlkwc{col}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{)}
+
+
+\hlkwd{legend}\hlstd{(}\hlstr{"topleft"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"<0.05 in DGINN-bats but >0.05 in Hawkins"}\hlstd{,}
+ \hlstr{"<0.05 in Hawkinsbut >0.05 in DGINN-bats"}\hlstd{),}
+ \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{))}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{figure/pvalM7M8compautre-1}
+
+\end{knitrout}
+
+
+
+
+
+\subsection{Diagramme de Venn}
+
+I will draw a venn diagramm for the positive genes in the 3 analyses.
+
+\subsubsection{subtab}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_PValue_PamlM7M8"}\hlstd{,} \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,} \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{)])}
+\hlkwd{dim}\hlstd{(tmp)}
+\end{alltt}
+\begin{verbatim}
+## [1] 154 4
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+154 genes (present in the 3 experiments)
+
+\subsubsection{figure}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{area1dginn}\hlkwb{<-}\hlkwd{sum}\hlstd{(tmp}\hlopt{$}\hlstd{bats_PValue_PamlM7M8}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlkwc{na.rm}\hlstd{=T)}
+\hlstd{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{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{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)}
+
+
+\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{))}
+\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])
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
\end{document}
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