\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
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\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
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\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
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\let\hlipl\hlkwb
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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.
%\geometry{letterpaper} % ... or a4paper or a5paper or ...
%\geometry{landscape} % Activate for for rotated page geometry
%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
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%\usepackage{amssymb}
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%\usepackage[cyr]{aeguill}
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%\usepackage{hyperref}
\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}