covid_comp_primate-Young-focus_backup.tex

\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
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\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb

\usepackage{framed}
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\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX

\usepackage{alltt}   	% use "amsart" instead of "article" for AMSLaTeX format
%\usepackage{geometry}                		% See geometry.pdf to learn the layout options. There are lots.
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\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou}
\date{October 2020}							% Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle

\tableofcontents

\newpage

\section{Files manipulations}

\subsection{Read Janet Young's table}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{workdir}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"}

\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
  \hlstr{"data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"}\hlstd{),}
        \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{","}\hlstd{)}
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\begin{verbatim}
## [1] 332  84
\end{verbatim}
\begin{alltt}
\hlcom{#names(tab)}
\end{alltt}
\end{kframe}
\end{knitrout}

\subsection{Read DGINN Young table}

DGINN-Young-primate table correspond to DGINN results, on the SAME alignment as Young-primate.

I will merge the 2 tables.

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{dginnY}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
  \hlstr{"data/summary_primate_young.res"}\hlstd{),}
        \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}

\hlkwd{dim}\hlstd{(dginnY)}
\end{alltt}
\begin{verbatim}
## [1] 1992    7
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnY)}
\end{alltt}
\begin{verbatim}
## [1] "Gene"    "Omega"   "Method"  "PosSel"  "PValue"  "NbSites" "PSS"
\end{verbatim}
\end{kframe}
\end{knitrout}


\subsection{Joining Young and DGINN Young table}

\textit{I hide some code corresponding to verifications of gene names coherence between tables}


\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{)\{}

\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstd{method,}
           \hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}

\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"Omega_"}\hlstd{, method),}
              \hlkwd{paste0}\hlstd{(}\hlstr{"PosSel_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PValue_"}\hlstd{, method),}
              \hlkwd{paste0}\hlstd{(}\hlstr{"NbSites_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PSS_"}\hlstd{, method))}

\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}

\hlkwd{return}\hlstd{(tab)}
\hlstd{\}}

\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM1M2"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM7M8"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM1M2"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM7M8"}\hlstd{)}


\hlcom{# Manip pour la colonne BUSTED}

\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\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{"Gene.name"}\hlstd{,} \hlstr{"Omega_BUSTED"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{,} \hlstr{"PValue_BUSTED"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}

\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\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{"Gene.name"}\hlstd{,} \hlstr{"NbSites_MEME"}\hlstd{,} \hlstr{"PSS_MEME"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}


\subsection{Read DGINN Table}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"/data/DGINN_202005281649summary_cleaned.csv"}\hlstd{),}
      \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}

\hlkwd{dim}\hlstd{(dginnT)}
\end{alltt}
\begin{verbatim}
## [1] 412  27
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnT)}
\end{alltt}
\begin{verbatim}
##  [1] "File"               "Name"               "Gene"               "GeneSize"           "NbSpecies"          "omegaM0Bpp"        
##  [7] "omegaM0codeml"      "BUSTED"             "BUSTED.p.value"     "MEME.NbSites"       "MEME.PSS"           "BppM1M2"           
## [13] "BppM1M2.p.value"    "BppM1M2.NbSites"    "BppM1M2.PSS"        "BppM7M8"            "BppM7M8.p.value"    "BppM7M8.NbSites"   
## [19] "BppM7M8.PSS"        "codemlM1M2"         "codemlM1M2.p.value" "codemlM1M2.NbSites" "codemlM1M2.PSS"     "codemlM7M8"        
## [25] "codemlM7M8.p.value" "codemlM7M8.NbSites" "codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
\hlcom{# Number of genes in dginn-primate output not present in the original table}
\hlstd{dginnT[(dginnT}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F,}\hlstr{"Gene"}\hlstd{]}
\end{alltt}
\begin{verbatim}
##  [1] ACE2               ADAM9[0-3120]      ADAM9[3119-3927]   ATP5MGL            C1H1ORF50          CEP135[0-3264]     CEP135[3263-3678] 
##  [8] CEP43              COQ8B              COQ8A              CSNK2A1            CSNK2B[0-609]      CSNK2B[608-2568]   CYB5R1            
## [15] DDX21[0-717]       DDX21[716-2538]    DDX50              DNAJC15            DPH5[0-702]        DPH5[701-1326]     DPY19L2           
## [22] ELOC               ERO1B              EXOSC3[0-1446]     EXOSC3[1445-1980]  FBN3               GNB4               GNB2              
## [29] GNB3               GOLGA7[0-312]      GOLGA7[311-549]    GPX1[0-1218]       GPX1[1217-2946]    HDAC1              HS6ST3            
## [36] IMPDH1             ITGB1[0-2328]      ITGB1[2327-2844]   LMAN2L             MRPS5[0-1569]      MRPS5[1568-3783]   MARC2             
## [43] MGRN1              NDFIP2[0-768]      NDFIP2[767-1314]   NDUFAF2[0-258]     NDUFAF2[257-744]   NSD2               NUP58             
## [50] NUP58[0-1824]      NUP58[1823-2367]   PABPC3             POTPABPC1          PABPC4L            PABPC5             PCSK5             
## [57] PRIM2[0-1071]      PRIM2[1070-1902]   PRKACB             PRKACG             PTGES2[0-1587]     PTGES2[1586-2202]  RAB8B             
## [64] RAB13              RAB18[0-855]       RAB18[854-1815]    RAB2B              RAB5A              RAB5B              RAB15             
## [71] RALB               EZR                EZR[0-1458]        EZR[1457-3771]     MSN                RETREG3            RHOB              
## [78] RHOC               SLC44A2[0-2577]    SLC44A2[2576-3657] SPART              SRP72[0-2604]      SRP72[2603-3417]   STOM[0-1047]      
## [85] STOM[1046-1800]    STOML3             TIMM29             TLE4               TLE2               TLE2[0-1302]       TLE2[1301-3987]   
## [92] TMPRSS2            TOMM70             TOR1B              WASHC4             WFS1[0-2346]       WFS1[2345-3216]    YIF1B             
## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ADAM9[0-3120] ADAM9[3119-3927] ADAMTS1 AES AGPS AKAP8 AKAP8L AKAP9 ... ZYG11B
\end{verbatim}
\begin{alltt}
\hlcom{# This includes paralogs, recombinations found by DGINN }
\hlcom{# and additionnal genes included on purpose}

\hlcom{# Number of genes from the original list not present in DGINN output}
\hlstd{tab[(tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F,}\hlstr{"Gene.name"}\hlstd{]}
\end{alltt}
\begin{verbatim}
##  [1] "ADCK4"    "ARL6IP6"  "ATP5L"    "C19orf52" "C1orf50"  "ERO1LB"   "FAM134C"  "FGFR1OP"  "KIAA1033" "MFGE8"    "NUPL1"    "SIGMAR1" 
## [13] "SPG20"    "TCEB1"    "TCEB2"    "TOMM70A"  "USP13"    "VIMP"     "WHSC1"
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,} \hlstr{"dginn-primate_NbSpecies"}\hlstd{,} \hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{,}
  \hlstr{"dginn-primate_omegaM0codeml"}\hlstd{,} \hlstr{"dginn-primate_BUSTED"}\hlstd{,} \hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{,}
  \hlstr{"dginn-primate_MEME.NbSites"}\hlstd{,}       \hlstr{"dginn-primate_MEME.PSS"}\hlstd{,}           \hlstr{"dginn-primate_BppM1M2"}\hlstd{,}
  \hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{,}    \hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{,}   \hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{,}
  \hlstr{"dginn-primate_BppM7M8"}\hlstd{,}            \hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{,}    \hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{,}
  \hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{,}        \hlstr{"dginn-primate_codemlM1M2"}\hlstd{,}         \hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{,}
  \hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{,}     \hlstr{"dginn-primate_codemlM7M8"}\hlstd{,}
  \hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}



\subsection{Join Table and DGINN table}


\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnT,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
\end{alltt}
\end{kframe}
\end{knitrout}


\subsection{Write new table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{write.table}\hlstd{(tab,}
        \hlstr{"COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20201014.txt"}\hlstd{,}
        \hlkwc{row.names}\hlstd{=F,} \hlkwc{quote}\hlstd{=F,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}













%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Comparisons Primates}

\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young'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{$}\hlstd{whole.gene.dN.dS.model.0, tab}\hlopt{$}\hlstd{Omega_PamlM7M8,}
     \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.2} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\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{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}

\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.6} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{>}\hlnum{0.7}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8-1} 

\end{knitrout}



\subsection{DGINN results on Janet Young's alignments (DGINN-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}
\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{))}
\end{alltt}


{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlkwd{plot}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{, tab}\hlopt{$}\hlstd{Omega_PamlM7M8,}
     \hlkwc{xlab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"Omega DGINN-Young-primate"}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}

\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{<}\hlnum{0.2}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{,}
\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}

\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.5} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{<}\hlnum{0.4}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{,}
\hlkwc{y}\hlstd{=(outlier}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{+}\hlnum{0.01}\hlstd{),}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8_2-1} 

\end{knitrout}


\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{$}\hlstd{whole.gene.dN.dS.model.0,} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{)),}
     \hlkwc{xlab}\hlstd{=}\hlstr{"Omega Young-primate"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"DGINN-full's"}\hlstd{)}
\hlkwd{abline}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{)}


\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.5}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn-primate_omegaM0Bpp'}\hlstd{,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8_3-1} 

\end{knitrout}


\section{Overlap}


\subsection{Mondrian}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(Mondrian)}

\hlcom{#######}

\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlkwd{dim}\hlstd{(monddata)}
\end{alltt}
\begin{verbatim}
## [1] 333   1
\end{verbatim}
\begin{alltt}
\hlstd{dginnyoungtmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstd{PosSel_PamlM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_PamlM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM1M2}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstd{PosSel_BUSTED}\hlopt{==}\hlstr{"Y"}\hlstd{))}

\hlcom{#monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)}


\hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_BUSTED'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn-primate_BppM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_BppM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'dginn-primate_codemlM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{, tab}\hlopt{$}\hlstr{'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{)}
\hlcom{#monddata$primates_cooper<-ifelse(tab$cooper.primates.M7.M8_p_val<0.05, 1, 0)}


\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\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{"DGINN-Young >=3"}\hlstd{,} \hlstr{"DGINN-full >=3"} \hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianprimates-1} 
\begin{kframe}\begin{alltt}
\hlcom{#####}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}

\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young >=4"}\hlstd{,} \hlstr{"DGINN-full >=4"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianprimates-2} 

\end{knitrout}

Comparison of results with the same method.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlcom{#####}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstd{PosSel_BppM7M8}\hlopt{==}\hlstr{"Y"}
\hlstd{monddata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}

\hlkwd{mondrian}\hlstd{(}\hlkwd{na.omit}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{4}\hlstd{]),} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Young"}\hlstd{,} \hlstr{"DGINN-Young"}\hlstd{,} \hlstr{"DGINN-full"}\hlstd{),} \hlkwc{main}\hlstd{=}\hlstr{"posel codeml M7M8"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/unnamed-chunk-8-1} 

\end{knitrout}

\subsection{subsetR}

Just another representation of the same result.

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(UpSetR)}
\hlstd{upsetdata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}



\hlstd{upsetdata}\hlopt{$}\hlstd{primates_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(tab}\hlopt{$}\hlstd{pVal.M8vsM7}\hlopt{<}\hlnum{0.05}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}

\hlcom{###}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}


\hlkwd{upset}\hlstd{(}\hlkwd{na.omit}\hlstd{(upsetdata),} \hlkwc{nsets} \hlstd{=} \hlnum{3}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/subsetprimates-1} 
\begin{kframe}\begin{alltt}
\hlcom{###}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnyoungtmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}

\hlkwd{upset}\hlstd{(}\hlkwd{na.omit}\hlstd{(upsetdata),} \hlkwc{nsets} \hlstd{=} \hlnum{3}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/subsetprimates-2} 

\end{knitrout}

\section{Gene List}

Genes under positive selection for at least 4 methods.

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{dginnfulltmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tab}\hlopt{$}\hlstr{'dginn-primate_BUSTED'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
 \hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_BppM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_BppM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_codemlM1M2'}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tab}\hlopt{$}\hlstr{'dginn-primate_codemlM7M8'}\hlopt{==}\hlstr{"Y"}\hlstd{))}

\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
\end{alltt}
\begin{verbatim}
##  [1] "ACADM"     "BCS1L"     "BRD4"      "CDK5RAP2"  "CEP135"    "CEP68"     "CLIP4"     "DNMT1"     "DPH5"      "EMC1"      "FYCO1"    
## [12] "GCC2"      "GGH"       "GHITM"     "GIGYF2"    "GLA"       "GOLGA7"    "HECTD1"    "IDE"       "ITGB1"     "LARP1"     "LARP4B"   
## [23] "LMAN2"     "MARK1"     "MIPOL1"    "MPHOSPH10" "MYCBP2"    "NDUFAF2"   "NDUFB9"    "PCNT"      "POLA1"     "PRIM2"     "PRKAR2A"  
## [34] "PVR"       "REEP6"     "RIPK1"     "SAAL1"     "SEPSECS"   "SIRT5"     "SLC25A21"  "SLC27A2"   "TMEM39B"   "TOR1AIP1"  "TUBGCP2"  
## [45] "UBAP2"     "UGGT2"     "VPS39"     "ZNF318"
\end{verbatim}
\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[dginnfulltmp}\hlopt{>=}\hlnum{3} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F]}
\end{alltt}
\begin{verbatim}
##  [1] "ACADM"     "ADAM9"     "AP2A2"     "ATE1"      "BCS1L"     "BRD4"      "BZW2"      "CDK5RAP2"  "CEP135"    "CEP68"     "CLIP4"    
## [12] "CNTRL"     "DNMT1"     "DPH5"      "EDEM3"     "EIF4E2"    "EMC1"      "EXOSC2"    "FYCO1"     "GCC2"      "GGH"       "GHITM"    
## [23] "GIGYF2"    "GLA"       "GOLGA7"    "GOLGB1"    "GORASP1"   "HDAC2"     "HECTD1"    "HS6ST2"    "IDE"       "ITGB1"     "LARP1"    
## [34] "LARP4B"    "LARP7"     "LMAN2"     "MARK1"     "MDN1"      "MIPOL1"    "MOV10"     "MPHOSPH10" "MRPS5"     "MYCBP2"    "NAT14"    
## [45] "NDUFAF2"   "NDUFB9"    "NGLY1"     "NPC2"      "PCNT"      "PITRM1"    "PLAT"      "PLOD2"     "PMPCB"     "POLA1"     "POR"      
## [56] "PRIM2"     "PRKAR2A"   "PTBP2"     "PVR"       "RAB14"     "RAB1A"     "RAB2A"     "RAP1GDS1"  "RBX1"      "REEP6"     "RIPK1"    
## [67] "RPL36"     "SAAL1"     "SCCPDH"    "SEPSECS"   "SIRT5"     "SLC25A21"  "SLC27A2"   "STOM"      "TIMM8B"    "TMEM39B"   "TOR1AIP1" 
## [78] "TRIM59"    "TRMT1"     "TUBGCP2"   "UBAP2"     "UGGT2"     "USP54"     "VPS39"     "ZNF318"
\end{verbatim}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tab[dginnfulltmp}\hlopt{>=}\hlnum{4} \hlopt{&} \hlkwd{is.na}\hlstd{(dginnfulltmp)}\hlopt{==}\hlstd{F,}
\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,}\hlstr{"dginn-primate_BUSTED"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2"}\hlstd{,}
 \hlstr{"dginn-primate_BppM7M8"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8"}\hlstd{)]}

\hlkwd{write.table}\hlstd{(tmp,} \hlstr{"geneList_DGINN_full_primate_pos4.txt"}\hlstd{,} \hlkwc{row.names}\hlstd{=F,} \hlkwc{quote}\hlstd{=F)}
\end{alltt}
\end{kframe}
\end{knitrout}


\section{Shiny like}

\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{makeFig1} \hlkwb{<-} \hlkwa{function}\hlstd{(}\hlkwc{df}\hlstd{)\{}

  \hlcom{# prepare data for colors etc}
  \hlstd{colMethods} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"deepskyblue4"}\hlstd{,} \hlstr{"darkorange"} \hlstd{,} \hlstr{"deepskyblue3"} \hlstd{,} \hlstr{"mediumseagreen"} \hlstd{,} \hlstr{"yellow3"} \hlstd{,} \hlstr{"black"}\hlstd{)}
  \hlstd{nameMethods} \hlkwb{<-} \hlkwd{c}\hlstd{(}\hlstr{"BUSTED"}\hlstd{,} \hlstr{"BppM1M2"}\hlstd{,} \hlstr{"BppM7M8"}\hlstd{,} \hlstr{"codemlM1M2"}\hlstd{,} \hlstr{"codemlM7M8"}\hlstd{,} \hlstr{"MEME"}\hlstd{)}
  \hlstd{metColor} \hlkwb{<-} \hlkwd{data.frame}\hlstd{(}\hlkwc{Name} \hlstd{= nameMethods ,} \hlkwc{Col} \hlstd{= colMethods ,} \hlkwc{stringsAsFactors} \hlstd{=} \hlnum{FALSE}\hlstd{)}

  \hlcom{# subset for this specific figure}
  \hlcom{#df <- df[df$nbY >= 1, ] # to drop genes found by 0 methods (big datasets)}
  \hlstd{xt} \hlkwb{<-} \hlstd{df[,} \hlkwd{c}\hlstd{(}\hlstr{"BUSTED"}\hlstd{,} \hlstr{"BppM1M2"}\hlstd{,} \hlstr{"BppM7M8"}\hlstd{,} \hlstr{"codemlM1M2"}\hlstd{,} \hlstr{"codemlM7M8"}\hlstd{)]}
  \hlstd{xt}\hlopt{$}\hlstd{Gene} \hlkwb{<-} \hlstd{df}\hlopt{$}\hlstd{Gene}
  \hlstd{nbrMeth} \hlkwb{<-} \hlnum{5}
  \hlcom{# reverse order of dataframe so that genes with the most Y are at the bottom (to be on top of the barplot)}
  \hlstd{xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]} \hlkwb{<-} \hlkwd{ifelse}\hlstd{(xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]} \hlopt{==} \hlstr{"Y"}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
  \hlcom{# sort and Filter the 0 lines}
  \hlstd{xt}\hlkwb{<-}\hlstd{xt[}\hlkwd{order}\hlstd{(}\hlkwd{rowSums}\hlstd{(xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{])),]}
  \hlstd{xt}\hlkwb{<-}\hlstd{xt[}\hlkwd{rowSums}\hlstd{(xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{])}\hlopt{>}\hlnum{2}\hlstd{,]}

  \hlkwd{row.names}\hlstd{(xt)}\hlkwb{<-}\hlstd{xt}\hlopt{$}\hlstd{Gene}
  \hlstd{xt}\hlkwb{<-}\hlstd{xt[,}\hlnum{1}\hlopt{:}\hlnum{5}\hlstd{]}

  \hlstd{colFig1} \hlkwb{<-} \hlstd{metColor[}\hlkwd{which}\hlstd{(metColor}\hlopt{$}\hlstd{Name} \hlopt{%in%} \hlkwd{colnames}\hlstd{(xt)) , ]}

  \hlcom{##### PART 1 : NUMBER OF METHODS}
  \hlkwd{par}\hlstd{(}\hlkwc{xpd} \hlstd{=} \hlnum{NA} \hlstd{,} \hlkwc{mar}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{2}\hlstd{,}\hlnum{7}\hlstd{,}\hlnum{4}\hlstd{,}\hlnum{0}\hlstd{) ,}   \hlkwc{oma} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{) ,} \hlkwc{mgp} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{3}\hlstd{,}\hlnum{0.3}\hlstd{,}\hlnum{0}\hlstd{))}

  \hlstd{h} \hlkwb{=}  \hlkwd{barplot}\hlstd{(}
    \hlkwd{t}\hlstd{(xt),}
    \hlkwc{border} \hlstd{=} \hlnum{NA} \hlstd{,}
    \hlkwc{axes} \hlstd{= F ,}
    \hlkwc{col} \hlstd{=} \hlkwd{adjustcolor}\hlstd{(colFig1}\hlopt{$}\hlstd{Col,} \hlkwc{alpha.f} \hlstd{=} \hlnum{1}\hlstd{),}
    \hlkwc{horiz} \hlstd{= T ,}
    \hlkwc{las}  \hlstd{=} \hlnum{2} \hlstd{,}
    \hlkwc{main} \hlstd{=} \hlstr{"Methods detecting positive selection"} \hlstd{,}
    \hlkwc{cex.main} \hlstd{=} \hlnum{0.85}\hlstd{,}
    \hlkwc{cex.names}  \hlstd{=} \hlkwd{min}\hlstd{(}\hlnum{50}\hlopt{/}\hlkwd{nrow}\hlstd{(xt),} \hlnum{1.5}\hlstd{)}
  \hlstd{)}

  \hlkwd{axis}\hlstd{(}\hlnum{3}\hlstd{,} \hlkwc{line} \hlstd{=} \hlnum{0}\hlstd{,} \hlkwc{at} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlopt{:}\hlstd{nbrMeth),} \hlkwc{label} \hlstd{=} \hlkwd{c}\hlstd{(}\hlstr{"0"}\hlstd{,} \hlkwd{rep}\hlstd{(}\hlstr{""}\hlstd{, nbrMeth} \hlopt{-}\hlnum{1}\hlstd{), nbrMeth),} \hlkwc{tck} \hlstd{=} \hlnum{0.02}\hlstd{)}

  \hlkwd{legend}\hlstd{(}\hlstr{"bottomleft"}\hlstd{,}
         \hlkwc{horiz} \hlstd{= T,}
         \hlkwc{border} \hlstd{= colFig1}\hlopt{$}\hlstd{Col,}
         \hlkwc{legend} \hlstd{= colFig1}\hlopt{$}\hlstd{Name,}
         \hlkwc{fill} \hlstd{= colFig1}\hlopt{$}\hlstd{Col,}
         \hlkwc{cex} \hlstd{=} \hlnum{0.8}\hlstd{,}
         \hlkwc{bty} \hlstd{=} \hlstr{"n"}\hlstd{,}
         \hlkwc{xpd} \hlstd{=} \hlnum{NA}
  \hlstd{)}
\hlstd{\}}


\hlstd{df}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"/data/DGINN_202005281649summary_cleaned.csv"}\hlstd{),}
      \hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}


\hlkwd{makeFig1}\hlstd{(df)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/shiny-1} 

\end{knitrout}

\end{document}