diff --git a/covid_comp_bats.Rnw b/covid_comp_bats.Rnw
index c399d8a7a7a57f7246c4cbbf0131b23060e617ef..4fd9177c002b6ae22f5bde1262f7d15bc60ffb77 100644
--- a/covid_comp_bats.Rnw
+++ b/covid_comp_bats.Rnw
@@ -62,8 +62,6 @@ y=as.numeric(as.character(outlier$bats_omegaM0codeml)),
outlier$Gene.name)
@
-\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
-
\section{Overlap}
\subsection{Data}
@@ -159,11 +157,8 @@ dftmp<-tab[,c("bats_File", "bats_Name",
names(dftmp)<-names(df)
makeFig1(dftmp)
-
@
-
-
\end{document}
diff --git a/covid_comp_primate.Rnw b/covid_comp_primate.Rnw
index d502adf3daecec1e63da7a98eacd83ceb4495e7f..44749ff82c1a9a682aacc52a65435c73cb4ac018 100644
--- a/covid_comp_primate.Rnw
+++ b/covid_comp_primate.Rnw
@@ -30,108 +30,166 @@
Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
<<>>=
-workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
+home<-"/home/adminmarie/Documents/"
+workdir<-paste0(home, "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$Gene.name<-as.character(tab$Gene.name.x)
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")
+<<omegaM7M8_1>>=
+tab$dginn.primate_omegaM0Bpp[tab$dginn.primate_omegaM0Bpp=="na"]<-NA
+tab$dginn.primate_omegaM0Bpp<-as.numeric(as.character(
+ tab$dginn.primate_omegaM0Bpp))
+
+plot(tab$whole.gene.dN.dS.model.0,
+ tab$dginn.primate_omegaM0Bpp,
+ xlab="Omega Young-primate",
+ ylab="DGINN-full's",
+ cex=0.3)
abline(0,1)
-abline(lm(as.numeric(as.character(tab$dginn.primate_omegaM0Bpp))~tab$whole.gene.dN.dS.model.0), col="red")
+abline(lm(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,]
+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$Gene.name)
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.1 &
+ tab$dginn.primate_omegaM0Bpp>0.3,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=outlier$dginn.primate_omegaM0Bpp,
+outlier$Gene.name)
+
+outlier<-tab[tab$whole.gene.dN.dS.model.0>0.33 &
+ tab$dginn.primate_omegaM0Bpp<0.2,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=outlier$dginn.primate_omegaM0Bpp,
+outlier$Gene.name)
+
+outlier<-tab[tab$whole.gene.dN.dS.model.0>0.6 &
+ tab$dginn.primate_omegaM0Bpp<0.6,]
+text(x=outlier$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")
+<<omegaM7M8_2>>=
+tab$cooper.primates.Average_dNdS<-as.numeric(as.character(
+ tab$cooper.primates.Average_dNdS))
+
+plot(tab$whole.gene.dN.dS.model.0,
+ tab$cooper.primates.Average_dNdS,
+ xlab="Omega Young-primate",
+ ylab="Omega Cooper-primate",
+ cex=0.3)
abline(0,1)
-abline(lm(as.numeric(as.character(tab$cooper.primates.Average_dNdS))~tab$whole.gene.dN.dS.model.0), col="red")
+abline(lm(tab$cooper.primates.Average_dNdS~tab$whole.gene.dN.dS.model.0),
+ col="red")
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.15 &
+ tab$cooper.primates.Average_dNdS>0.4,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=outlier$cooper.primates.Average_dNdS,
+outlier$Gene.name, cex=0.5)
-outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 & tab$cooper.primates.Average_dNdS>0.5,]
+outlier<-tab[tab$whole.gene.dN.dS.model.0<0.3 &
+ 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)
+outlier$Gene.name, cex=0.5)
+outlier<-tab[tab$whole.gene.dN.dS.model.0>0.3 &
+ tab$cooper.primates.Average_dNdS<0.1,]
+text(x=outlier$whole.gene.dN.dS.model.0,
+y=outlier$cooper.primates.Average_dNdS,
+outlier$Gene.name, cex=0.5)
@
\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")
+<<omegaM7M8_3>>=
+plot(tab$cooper.primates.Average_dNd,
+ tab$dginn.primate_omegaM0Bpp,
+ xlab="Omega Cooper-primate",
+ ylab="DGINN-full's",
+ cex=0.3)
abline(0,1)
-abline(lm(as.numeric(as.character(tab$dginn.primate_omegaM0Bpp))~tab$cooper.primates.Average_dNd), col="red")
+abline(lm(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,]
+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$Gene.name)
-
-@
-
-
+outlier$Gene.name, cex=0.5)
+outlier<-tab[tab$cooper.primates.Average_dNd<0.1 &
+ tab$dginn.primate_omegaM0Bpp>0.3,]
+text(x=outlier$cooper.primates.Average_dNd,
+y=outlier$dginn.primate_omegaM0Bpp,
+outlier$Gene.name, cex=0.5)
+outlier<-tab[tab$cooper.primates.Average_dNd>0.7 &
+ tab$dginn.primate_omegaM0Bpp<0.3,]
+text(x=outlier$cooper.primates.Average_dNd,
+y=outlier$dginn.primate_omegaM0Bpp,
+outlier$Gene.name, cex=0.5)
+outlier<-tab[tab$cooper.primates.Average_dNd>0.45 &
+ tab$dginn.primate_omegaM0Bpp<0.2,]
+text(x=outlier$cooper.primates.Average_dNd,
+y=outlier$dginn.primate_omegaM0Bpp,
+outlier$Gene.name, cex=0.5)
+@
\section{Overlap}
-
\subsection{Mondrian}
<<mondrianprimates>>=
-
library(Mondrian)
-#######
-
monddata<-as.data.frame(tab$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$dginn.primate_codemlM7M8=="Y"))
-dginnfulltmp<-rowSums(cbind(tab$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$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
+monddata$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" ))
+mondrian(na.omit(monddata[,2:4]),
+ labels=c("Young", "Cooper", "DGINN-full >=3" ))
-#####
-monddata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0)
+monddata$primates_dginn_full<-ifelse(
+ dginnfulltmp>=4, 1,0)
-mondrian(na.omit(monddata[,2:4]), labels=c("Young", "Cooper", "DGINN-full >=4"))
+mondrian(na.omit(monddata[,2:4]),
+ labels=c("Young", "Cooper", "DGINN-full >=4"))
@
@@ -144,7 +202,8 @@ 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$cooper.primates.M7.M8_p_value<0.05, 1, 0)
+upsetdata$primate_cooper<-ifelse(
+ tab$cooper.primates.M7.M8_p_value<0.05, 1, 0)
upsetdata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
diff --git a/covid_comp_primate.pdf b/covid_comp_primate.pdf
index 0840330fbd5d2c6fb016cec3aadd243fb8922118..d7e4d15dc84753caebeb142c080c1b6b0653e9cb 100644
Binary files a/covid_comp_primate.pdf and b/covid_comp_primate.pdf differ
diff --git a/covid_comp_primate.tex b/covid_comp_primate.tex
index 145593b25b82c3ee2d452c4438f9253dc1cc5cd8..ee3f1f28f46b4f39dbf10e17f0548e847434f0d5 100644
--- a/covid_comp_primate.tex
+++ b/covid_comp_primate.tex
@@ -82,51 +82,65 @@ 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{home}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/"}
+\hlstd{workdir}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"CIRI_BIBS_projects/2020_05_Etienne_covid/"}\hlstd{)}
\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
+## [1] 332 141
\end{verbatim}
\begin{alltt}
-\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name.x)}
\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}
+\hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp[tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{==}\hlstr{"na"}\hlstd{]}\hlkwb{<-}\hlnum{NA}
+\hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp))}
+
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,}
+ \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{,}
+ \hlkwc{cex}\hlstd{=}\hlnum{0.3}\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{$}\hlstd{dginn.primate_omegaM0Bpp))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
-\end{alltt}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{~}\hlstd{tab}\hlopt{$}\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{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.5}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning in eval(predvars, data, env): NAs introduits lors de la conversion automatique}}\begin{alltt}
-\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.5}\hlstd{,]}
-\end{alltt}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.1} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.3}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{>}\hlnum{0.33} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{<}\hlnum{0.2}\hlstd{,]}
+\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{$}\hlstd{Gene.name)}
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning in Ops.factor(tab\$dginn.primate\_omegaM0Bpp, 0.5): '>' not meaningful for factors}}\begin{alltt}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{>}\hlnum{0.6} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{<}\hlnum{0.6}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
@@ -139,19 +153,39 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" d
\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{)}
+\hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS))}
+
+\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,}
+ \hlkwc{ylab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{,}
+ \hlkwc{cex}\hlstd{=}\hlnum{0.3}\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{)}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\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{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.15} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS}\hlopt{>}\hlnum{0.4}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
-\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS}\hlopt{>}\hlnum{0.5}\hlstd{,]}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.3} \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)}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{>}\hlnum{0.3} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNdS}\hlopt{<}\hlnum{0.1}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.primates.Average_dNdS,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8_2-1}
@@ -161,43 +195,49 @@ Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.p
\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{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd,}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-primate"}\hlstd{,}
+ \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{,}
+ \hlkwc{cex}\hlstd{=}\hlnum{0.3}\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{$}\hlstd{dginn.primate_omegaM0Bpp))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
-\end{alltt}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\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{,]}
+\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{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning in eval(predvars, data, env): NAs introduits lors de la conversion automatique}}\begin{alltt}
-\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.5}\hlstd{,]}
-\end{alltt}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd}\hlopt{<}\hlnum{0.1} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{>}\hlnum{0.3}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.primates.Average_dNd,}
+\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd}\hlopt{>}\hlnum{0.7} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{<}\hlnum{0.3}\hlstd{,]}
+\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{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning in Ops.factor(tab\$dginn.primate\_omegaM0Bpp, 0.5): '>' not meaningful for factors}}\begin{alltt}
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{cooper.primates.Average_dNd}\hlopt{>}\hlnum{0.45} \hlopt{&}
+ \hlstd{tab}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp}\hlopt{<}\hlnum{0.2}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.primates.Average_dNd,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstd{dginn.primate_omegaM0Bpp,}
-\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name,} \hlkwc{cex}\hlstd{=}\hlnum{0.5}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8_3-1}
\end{knitrout}
-
-
-
-
-
\section{Overlap}
-
\subsection{Mondrian}
\begin{knitrout}
@@ -205,8 +245,6 @@ Comparaison des Omega: colonne "cooper.primates.Average\_dNdS" VS colonne "omega
\begin{alltt}
\hlkwd{library}\hlstd{(Mondrian)}
-\hlcom{#######}
-
\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlkwd{dim}\hlstd{(monddata)}
\end{alltt}
@@ -214,22 +252,30 @@ Comparaison des Omega: colonne "cooper.primates.Average\_dNdS" VS colonne "omega
## [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{))}
+\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{$}\hlstd{dginn.primate_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+
+\hlstd{monddata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \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{(}
+ \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{(}
+ \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{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \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{))}
+\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}
@@ -248,7 +294,8 @@ Just another representation of the same result.
\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{primate_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \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{)}
@@ -287,14 +334,14 @@ Genes under positive selection for at least 4 methods.
\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"
+## [11] "ERO1LB" "FYCO1" "GCC2" "GGH" "GHITM"
+## [16] "GIGYF2" "GLA" "GOLGA7" "HECTD1" "IDE"
+## [21] "ITGB1" "LARP1" "LARP4B" "LMAN2" "MARK1"
+## [26] "MIPOL1" "MPHOSPH10" "MYCBP2" "NDUFAF2" "NDUFB9"
+## [31] "NUPL1" "PCNT" "POLA1" "PRIM2" "PRKAR2A"
+## [36] "PVR" "REEP6" "RIPK1" "SAAL1" "SEPSECS"
+## [41] "SIRT5" "SLC25A21" "SLC27A2" "TMEM39B" "TOR1AIP1"
+## [46] "TUBGCP2" "UBAP2" "UGGT2" "VPS39" "ZNF318"
\end{verbatim}
\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{3} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
@@ -303,20 +350,21 @@ Genes under positive selection for at least 4 methods.
## [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"
+## [16] "EIF4E2" "EMC1" "ERO1LB" "EXOSC2" "FYCO1"
+## [21] "GCC2" "GGH" "GHITM" "GIGYF2" "GLA"
+## [26] "GOLGA7" "GOLGB1" "GORASP1" "HDAC2" "HECTD1"
+## [31] "HS6ST2" "IDE" "ITGB1" "LARP1" "LARP4B"
+## [36] "LARP7" "LMAN2" "MARK1" "MDN1" "MIPOL1"
+## [41] "MOV10" "MPHOSPH10" "MRPS5" "MYCBP2" "NAT14"
+## [46] "NDUFAF2" "NDUFB9" "NGLY1" "NPC2" "NUPL1"
+## [51] "PCNT" "PITRM1" "PLAT" "PLOD2" "PMPCB"
+## [56] "POLA1" "POR" "PRIM2" "PRKAR2A" "PTBP2"
+## [61] "PVR" "RAB14" "RAB1A" "RAB2A" "RAP1GDS1"
+## [66] "RBX1" "REEP6" "RIPK1" "RPL36" "SAAL1"
+## [71] "SCCPDH" "SEPSECS" "SIRT5" "SLC25A21" "SLC27A2"
+## [76] "STOM" "TIMM8B" "TMEM39B" "TOR1AIP1" "TRIM59"
+## [81] "TRMT1" "TUBGCP2" "UBAP2" "UGGT2" "USP54"
+## [86] "VPS39" "ZNF318"
\end{verbatim}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tab[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F,}
diff --git a/figure/mondrianprimates-1.pdf b/figure/mondrianprimates-1.pdf
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