diff --git a/covid_comp_bats.Rnw b/covid_comp_bats.Rnw
index 279c190894cf75ffb6be9da2fd1f69cb28da075e..c399d8a7a7a57f7246c4cbbf0131b23060e617ef 100644
--- a/covid_comp_bats.Rnw
+++ b/covid_comp_bats.Rnw
@@ -15,7 +15,7 @@
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou}
-\date{janvier 2021} % Activate to display a given date or no date
+\date{Mars 2021} % Activate to display a given date or no date
\begin{document}
\maketitle
@@ -29,12 +29,13 @@
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"
@
@@ -43,25 +44,40 @@ tab$Gene.name[tab$PreyGene=="MTARC1"]<-"MTARC1"
\subsection{Cooper-bats results VS DGINN-bats results}
<<omegaM7M8bats>>=
+tab$bats_omegaM0codeml[tab$bats_omegaM0codeml=="na"]<-NA
-plot(tab$cooper.batsAverage_dNdS, as.numeric(as.character(tab$bats_omegaM0codeml)),
- xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
+plot(tab$cooper.batsAverage_dNdS,
+ as.numeric(as.character(tab$bats_omegaM0codeml)),
+ xlab="Omega Cooper-bats",
+ ylab="Omega DGINN-bats")
abline(0,1)
-abline(lm(as.numeric(as.character(tab$bats_omegaM0codeml))~tab$cooper.batsAverage_dNdS), col="red")
+abline(lm(as.numeric(as.character(tab$bats_omegaM0codeml))~
+ tab$cooper.batsAverage_dNdS),
+ col="red")
+
+outlier<-tab[tab$cooper.batsAverage_dNdS>0.35 &
+ as.numeric(as.character(tab$bats_omegaM0codeml))<0.3,]
+text(x=outlier$cooper.batsAverage_dNdS,
+y=as.numeric(as.character(outlier$bats_omegaM0codeml)),
+outlier$Gene.name)
@
\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
-\textit{I don't think we have the omega values}
-
\section{Overlap}
\subsection{Data}
<<subbats>>=
-tmp<-na.omit(tab[,c("Gene.name", "bats_codemlM7M8_p.value", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value", "bats_BUSTED", "bats_BppM1M2", "bats_BppM7M8", "bats_codemlM1M2", "bats_codemlM7M8")])
-
-tmp$bats_codemlM7M8_p.value<-as.numeric(as.character(tmp$bats_codemlM7M8_p.value))
+tmp<-na.omit(tab[,c("Gene.name", "bats_codemlM7M8_p.value",
+ "hawkins_Positive.Selection..M8vM8a.p.value",
+ "cooper.batsM7.M8_p_value", "bats_BUSTED",
+ "bats_BppM1M2", "bats_BppM7M8", "bats_codemlM1M2",
+ "bats_codemlM7M8")])
+
+tmp$bats_codemlM7M8_p.value[tmp$bats_codemlM7M8_p.value=="na"]<-NA
+tmp$bats_codemlM7M8_p.value<-as.numeric(
+ as.character(tmp$bats_codemlM7M8_p.value))
dim(tmp)
@
@@ -73,18 +89,25 @@ dim(tmp)
library(Mondrian)
monddata<-as.data.frame(tmp$Gene.name)
-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)
+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)
-dginntmp<-rowSums(cbind(tmp$bats_codemlM1M2=="Y", tmp$bats_codemlM7M8=="Y",
-tmp$bats_BppM1M2=="Y", tmp$bats_BppM7M8=="Y", tmp$bats_BUSTED=="Y"))
+dginntmp<-rowSums(cbind(tmp$bats_codemlM1M2=="Y",
+ tmp$bats_codemlM7M8=="Y",
+ tmp$bats_BppM1M2=="Y",
+ tmp$bats_BppM7M8=="Y",
+ tmp$bats_BUSTED=="Y"))
monddata$bats_dginn<-ifelse(dginntmp>=3, 1,0)
-mondrian(monddata[,2:4], labels=c("DGINN >=3", "hawkins", "Cooper"))
+mondrian(monddata[,2:4],
+ labels=c("DGINN >=3", "hawkins", "Cooper"))
monddata$bats_dginn<-ifelse(dginntmp>=4, 1,0)
-mondrian(monddata[,2:4], labels=c("DGINN >=4", "hawkins", "Cooper"))
+mondrian(monddata[,2:4],
+ labels=c("DGINN >=4", "hawkins", "Cooper"))
@
\subsection{subsetR}
@@ -93,8 +116,10 @@ mondrian(monddata[,2:4], labels=c("DGINN >=4", "hawkins", "Cooper"))
library(UpSetR)
upsetdata<-as.data.frame(tmp$Gene.name)
-upsetdata$bats_hawkins<-ifelse(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
-upsetdata$bats_cooper<-ifelse(tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
+upsetdata$bats_hawkins<-ifelse(
+ tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
+upsetdata$bats_cooper<-ifelse(
+ tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
upsetdata$bats_dginn<-ifelse(dginntmp>=3, 1,0)
@@ -117,15 +142,20 @@ df<-read.delim(paste0(workdir,
fill=T, h=T, sep=",")
names(df)
-dftmp<-tab[,c("bats_File", "bats_Name", "Gene.name",
- "bats_GeneSize", "bats_NbSpecies", "bats_omegaM0Bpp",
- "bats_omegaM0codeml", "bats_BUSTED", "bats_BUSTED_p.value",
- "bats_MEME_NbSites", "bats_MEME_PSS", "bats_BppM1M2",
- "bats_BppM1M2_p.value", "bats_BppM1M2_NbSites", "bats_BppM1M2_PSS",
- "bats_BppM7M8", "bats_BppM7M8_p.value", "bats_BppM7M8_NbSites",
- "bats_BppM7M8_PSS", "bats_codemlM1M2", "bats_codemlM1M2_p.value",
- "bats_codemlM1M2_NbSites","bats_codemlM1M2_PSS", "bats_codemlM7M8",
- "bats_codemlM7M8_p.value", "bats_codemlM7M8_NbSites" , "bats_codemlM7M8_PSS")]
+dftmp<-tab[,c("bats_File", "bats_Name",
+ "Gene.name", "bats_GeneSize",
+ "bats_NbSpecies", "bats_omegaM0Bpp",
+ "bats_omegaM0codeml", "bats_BUSTED",
+ "bats_BUSTED_p.value", "bats_MEME_NbSites",
+ "bats_MEME_PSS", "bats_BppM1M2",
+ "bats_BppM1M2_p.value", "bats_BppM1M2_NbSites",
+ "bats_BppM1M2_PSS", "bats_BppM7M8",
+ "bats_BppM7M8_p.value", "bats_BppM7M8_NbSites",
+ "bats_BppM7M8_PSS", "bats_codemlM1M2",
+ "bats_codemlM1M2_p.value", "bats_codemlM1M2_NbSites",
+ "bats_codemlM1M2_PSS", "bats_codemlM7M8",
+ "bats_codemlM7M8_p.value", "bats_codemlM7M8_NbSites" ,
+ "bats_codemlM7M8_PSS")]
names(dftmp)<-names(df)
makeFig1(dftmp)
diff --git a/covid_comp_bats.pdf b/covid_comp_bats.pdf
index ccdf459f9ee0c1633b0d1494840891dec816e06b..96b55dc51b6e79ec25fd3b9d2b42fc27d11af741 100644
Binary files a/covid_comp_bats.pdf and b/covid_comp_bats.pdf differ
diff --git a/covid_comp_bats.tex b/covid_comp_bats.tex
index 492243c8a5276216ead8510bb5045919d59f19a1..f30ce6c2f85fca9f23b5ddf1d8c75269c5a2f381 100644
--- a/covid_comp_bats.tex
+++ b/covid_comp_bats.tex
@@ -65,7 +65,7 @@
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou}
-\date{janvier 2021} % Activate to display a given date or no date
+\date{Mars 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle
@@ -81,17 +81,18 @@ 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}
@@ -104,26 +105,30 @@ 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}
-\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0codeml)),}
- \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-bats"}\hlstd{)}
-\end{alltt}
-
+\hlstd{tab}\hlopt{$}\hlstd{bats_omegaM0codeml[tab}\hlopt{$}\hlstd{bats_omegaM0codeml}\hlopt{==}\hlstr{"na"}\hlstd{]}\hlkwb{<-}\hlnum{NA}
-{\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{$}\hlstd{cooper.batsAverage_dNdS,}
+ \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0codeml)),}
+ \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Cooper-bats"}\hlstd{,}
+ \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-bats"}\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{$}\hlstd{bats_omegaM0codeml))}\hlopt{~}\hlstd{tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS),} \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+\hlkwd{abline}\hlstd{(}\hlkwd{lm}\hlstd{(}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0codeml))}\hlopt{~}
+ \hlstd{tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS),}
+ \hlkwc{col}\hlstd{=}\hlstr{"red"}\hlstd{)}
+
+\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{cooper.batsAverage_dNdS}\hlopt{>}\hlnum{0.35} \hlopt{&}
+ \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{bats_omegaM0codeml))}\hlopt{<}\hlnum{0.3}\hlstd{,]}
+\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{cooper.batsAverage_dNdS,}
+\hlkwc{y}\hlstd{=}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(outlier}\hlopt{$}\hlstd{bats_omegaM0codeml)),}
+\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\end{alltt}
-
-
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning in eval(predvars, data, env): NAs introduits lors de la conversion automatique}}\end{kframe}
+\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8bats-1}
\end{knitrout}
\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
-\textit{I don't think we have the omega values}
-
\section{Overlap}
\subsection{Data}
@@ -131,17 +136,19 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
-\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_codemlM7M8_p.value"}\hlstd{,} \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,} \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,} \hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{)])}
-
-\hlstd{tmp}\hlopt{$}\hlstd{bats_codemlM7M8_p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8_p.value))}
-\end{alltt}
-
-
-{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
+\hlstd{tmp}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(tab[,}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_codemlM7M8_p.value"}\hlstd{,}
+ \hlstr{"hawkins_Positive.Selection..M8vM8a.p.value"}\hlstd{,}
+ \hlstr{"cooper.batsM7.M8_p_value"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,}
+ \hlstr{"bats_BppM1M2"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,} \hlstr{"bats_codemlM1M2"}\hlstd{,}
+ \hlstr{"bats_codemlM7M8"}\hlstd{)])}
+
+\hlstd{tmp}\hlopt{$}\hlstd{bats_codemlM7M8_p.value[tmp}\hlopt{$}\hlstd{bats_codemlM7M8_p.value}\hlopt{==}\hlstr{"na"}\hlstd{]}\hlkwb{<-}\hlnum{NA}
+\hlstd{tmp}\hlopt{$}\hlstd{bats_codemlM7M8_p.value}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}
+ \hlkwd{as.character}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM7M8_p.value))}
\hlkwd{dim}\hlstd{(tmp)}
\end{alltt}
\begin{verbatim}
-## [1] 170 9
+## [1] 174 9
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -156,21 +163,28 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwd{library}\hlstd{(Mondrian)}
\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
-\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{)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{monddata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
-\hlstd{dginntmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
-\hlstd{tmp}\hlopt{$}\hlstd{bats_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstd{bats_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}
+\hlstd{dginntmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstd{bats_codemlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+ \hlstd{tmp}\hlopt{$}\hlstd{bats_codemlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+ \hlstd{tmp}\hlopt{$}\hlstd{bats_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+ \hlstd{tmp}\hlopt{$}\hlstd{bats_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
+ \hlstd{tmp}\hlopt{$}\hlstd{bats_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
-\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN >=3"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"Cooper"}\hlstd{))}
+\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{],}
+ \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN >=3"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"Cooper"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianbats-1}
\begin{kframe}\begin{alltt}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
-\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN >=4"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"Cooper"}\hlstd{))}
+\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{],}
+ \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN >=4"}\hlstd{,} \hlstr{"hawkins"}\hlstd{,} \hlstr{"Cooper"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianbats-2}
@@ -185,8 +199,10 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwd{library}\hlstd{(UpSetR)}
\hlstd{upsetdata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
-\hlstd{upsetdata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
-\hlstd{upsetdata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{upsetdata}\hlopt{$}\hlstd{bats_hawkins}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \hlstd{tmp}\hlopt{$}\hlstd{hawkins_Positive.Selection..M8vM8a.p.value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
+\hlstd{upsetdata}\hlopt{$}\hlstd{bats_cooper}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}
+ \hlstd{tmp}\hlopt{$}\hlstd{cooper.batsM7.M8_p_value}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
\hlstd{upsetdata}\hlopt{$}\hlstd{bats_dginn}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginntmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
@@ -230,15 +246,20 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
-\hlstd{dftmp}\hlkwb{<-}\hlstd{tab[,}\hlkwd{c}\hlstd{(}\hlstr{"bats_File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,}
- \hlstr{"bats_GeneSize"}\hlstd{,} \hlstr{"bats_NbSpecies"}\hlstd{,} \hlstr{"bats_omegaM0Bpp"}\hlstd{,}
- \hlstr{"bats_omegaM0codeml"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,} \hlstr{"bats_BUSTED_p.value"}\hlstd{,}
- \hlstr{"bats_MEME_NbSites"}\hlstd{,} \hlstr{"bats_MEME_PSS"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,}
- \hlstr{"bats_BppM1M2_p.value"}\hlstd{,} \hlstr{"bats_BppM1M2_NbSites"}\hlstd{,} \hlstr{"bats_BppM1M2_PSS"}\hlstd{,}
- \hlstr{"bats_BppM7M8"}\hlstd{,} \hlstr{"bats_BppM7M8_p.value"}\hlstd{,} \hlstr{"bats_BppM7M8_NbSites"}\hlstd{,}
- \hlstr{"bats_BppM7M8_PSS"}\hlstd{,} \hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM1M2_p.value"}\hlstd{,}
- \hlstr{"bats_codemlM1M2_NbSites"}\hlstd{,}\hlstr{"bats_codemlM1M2_PSS"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{,}
- \hlstr{"bats_codemlM7M8_p.value"}\hlstd{,} \hlstr{"bats_codemlM7M8_NbSites"} \hlstd{,} \hlstr{"bats_codemlM7M8_PSS"}\hlstd{)]}
+\hlstd{dftmp}\hlkwb{<-}\hlstd{tab[,}\hlkwd{c}\hlstd{(}\hlstr{"bats_File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,}
+ \hlstr{"Gene.name"}\hlstd{,} \hlstr{"bats_GeneSize"}\hlstd{,}
+ \hlstr{"bats_NbSpecies"}\hlstd{,} \hlstr{"bats_omegaM0Bpp"}\hlstd{,}
+ \hlstr{"bats_omegaM0codeml"}\hlstd{,} \hlstr{"bats_BUSTED"}\hlstd{,}
+ \hlstr{"bats_BUSTED_p.value"}\hlstd{,} \hlstr{"bats_MEME_NbSites"}\hlstd{,}
+ \hlstr{"bats_MEME_PSS"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,}
+ \hlstr{"bats_BppM1M2_p.value"}\hlstd{,} \hlstr{"bats_BppM1M2_NbSites"}\hlstd{,}
+ \hlstr{"bats_BppM1M2_PSS"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,}
+ \hlstr{"bats_BppM7M8_p.value"}\hlstd{,} \hlstr{"bats_BppM7M8_NbSites"}\hlstd{,}
+ \hlstr{"bats_BppM7M8_PSS"}\hlstd{,} \hlstr{"bats_codemlM1M2"}\hlstd{,}
+ \hlstr{"bats_codemlM1M2_p.value"}\hlstd{,} \hlstr{"bats_codemlM1M2_NbSites"}\hlstd{,}
+ \hlstr{"bats_codemlM1M2_PSS"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{,}
+ \hlstr{"bats_codemlM7M8_p.value"}\hlstd{,} \hlstr{"bats_codemlM7M8_NbSites"} \hlstd{,}
+ \hlstr{"bats_codemlM7M8_PSS"}\hlstd{)]}
\hlkwd{names}\hlstd{(dftmp)}\hlkwb{<-}\hlkwd{names}\hlstd{(df)}
\hlkwd{makeFig1}\hlstd{(dftmp)}
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