Forked from
mcariou / 2020_dginn_covid19
10 commits behind the upstream repository.
covid_comp_primate-Young-focus.tex 24.05 KiB
\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
% maxwidth is the original width if it is less than linewidth
% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\makeatletter
\def\maxwidth{ %
\ifdim\Gin@nat@width>\linewidth
\linewidth
\else
\Gin@nat@width
\fi
}
\makeatother
\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb
\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
\def\at@end@of@kframe{}%
\ifinner\ifhmode%
\def\at@end@of@kframe{\end{minipage}}%
\begin{minipage}{\columnwidth}%
\fi\fi%
\def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
\colorbox{shadecolor}{##1}\hskip-\fboxsep
% There is no \\@totalrightmargin, so:
\hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
\MakeFramed {\advance\hsize-\width
\@totalleftmargin\z@ \linewidth\hsize
\@setminipage}}%
{\par\unskip\endMakeFramed%
\at@end@of@kframe}
\makeatother
\definecolor{shadecolor}{rgb}{.97, .97, .97}
\definecolor{messagecolor}{rgb}{0, 0, 0}
\definecolor{warningcolor}{rgb}{1, 0, 1}
\definecolor{errorcolor}{rgb}{1, 0, 0}
\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
%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
% TeX will automatically convert eps --> pdf in pdflatex
%\usepackage{amssymb}
\usepackage[utf8]{inputenc}
%\usepackage[cyr]{aeguill}
%\usepackage[francais]{babel}
%\usepackage{hyperref}
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou}
\date{February 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}\maketitle
\tableofcontents
\newpage
\section{Files manipulations}
\subsection{Complete 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{"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] 332 141
\end{verbatim}
\begin{alltt}
\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{"MARC1"}\hlstd{]}\hlkwb{<-}\hlstr{"MARC1"}
\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"
## [7] "PSS"
\end{verbatim}
\end{kframe}
\end{knitrout}
\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{$}\hlstd{Method}\hlopt{==}\hlstr{"MEME"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}
\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"NbSites_MEME"}\hlstd{,} \hlstr{"PSS_MEME"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\begin{verbatim}
## [1] 332 167
\end{verbatim}
\end{kframe}
\end{knitrout}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Comparisons Primates}
\subsection{DGINN results on Janet Young's alignments (DGINN-Young-primate) VS Janet Young's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0))}\hlkwd{plot}\hlstd{(tab}\hlopt{$}\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{$}\hlstd{Gene.name)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlopt{>}\hlnum{0.2} \hlopt{&} \hlstd{tab}\hlopt{$}\hlstd{Omega_PamlM7M8}\hlopt{>}\hlnum{0.6}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\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{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.4} \hlopt{&} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\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{$}\hlstd{Gene.name)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{>}\hlnum{0.7} \hlopt{&} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\hlstd{outlier}\hlkwb{<-}\hlstd{tab[tab}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{<}\hlnum{0.1} \hlopt{&} \hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{))}\hlopt{>}\hlnum{0.3}\hlstd{,]}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=outlier}\hlopt{$}\hlstd{whole.gene.dN.dS.model.0}\hlopt{+}\hlnum{0.03}\hlstd{,}
\hlkwc{y}\hlstd{=outlier}\hlopt{$}\hlstr{'dginn.primate_omegaM0Bpp'}\hlstd{,}
\hlstd{outlier}\hlopt{$}\hlstd{Gene.name)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/omegaM7M8_3-1}
\end{knitrout}
\section{Overlap}
\subsection{Mondrian}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(Mondrian)}
\hlstd{monddata}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlkwd{dim}\hlstd{(monddata)}
\end{alltt}
\begin{verbatim}
## [1] 332 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}
\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-4-1}
\end{knitrout}
\subsection{subsetR}
Just another representation of the same result, for now, I focuse on the gene positive in 3 methodes for DGINN analysis.
\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{$}\hlstd{primates_dginn_full}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(dginnfulltmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlkwd{upset}\hlstd{(}\hlkwd{na.omit}\hlstd{(upsetdata),} \hlkwc{nsets} \hlstd{=} \hlnum{3}\hlstd{,} \hlkwc{matrix.color} \hlstd{=} \hlstr{"#DC267F"}\hlstd{,}
\hlkwc{main.bar.color} \hlstd{=} \hlstr{"#648FFF"}\hlstd{,} \hlkwc{sets.bar.color} \hlstd{=} \hlstr{"#FE6100"}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/subsetprimates-1}
\end{knitrout}
\section{Gene List}
List of the 34 genes found under positive selection in all analysis.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{TRUE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] ACADM ATE1 BCS1L BRD4 CDK5RAP2 CEP68
## [7] CNTRL DNMT1 EDEM3 FYCO1 GCC2 GHITM
## [13] GIGYF2 GOLGB1 GORASP1 ITGB1 MDN1 MPHOSPH10
## [19] MRPS5 NDUFAF2 PCNT PLAT POLA1 PRIM2
## [25] PVR SAAL1 SEPSECS SIRT5 SLC25A21 SLC27A2
## [31] TOR1AIP1 UGGT2 USP54 ZNF318
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
List of the 13 genes found under positive selection in both Young analysis and DGINN-Young alignments (but not full-DGINN).
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{FALSE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] ABCC1 ALG8 CEP250 CEP350 ERLEC1 FASTKD5 GOLGA2 MRPS27
## [9] NINL PDE4DIP PRRC2B RAB18 WFS1 ## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
List of the 1 gene found under positive selection in both DGINN analysis, but not Young.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{FALSE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{TRUE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] MARK1
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
List of the 8 genes found under positive selection in both Young analysis and full-DGINN, but not DGINN-young.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{FALSE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{TRUE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] <NA> LMAN2 NDUFB9 RIPK1 STOM TMEM39B TRMT1 UBAP2
## [9] VPS39
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
List of the 18 genes found under positive selection ONLY in Young analysis.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{FALSE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{FALSE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] AKAP9 ALG11 ALG5 C19orf52 CENPF CHMP2A COLGALT1
## [8] DCTPP1 DDX21 FBN1 FBXL12 JAKMIP1 <NA> NLRX1
## [15] NUP210 NUP98 PCSK6 PUSL1 ZYG11B
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
List of the 1 genes found under positive selection ONLY in DGINN-Young.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{FALSE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{TRUE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{FALSE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] FBN2
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
List of the 44 genes found under positive selection ONLY in full-DGINN.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}\hlstd{upsetdata}\hlopt{$}\hlstd{`tab$Gene.name`[(upsetdata}\hlopt{$}\hlstd{primates_young}\hlopt{==}\hlnum{FALSE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_young}\hlopt{==}\hlnum{FALSE} \hlopt{&}
\hlstd{upsetdata}\hlopt{$}\hlstd{primates_dginn_full}\hlopt{==}\hlnum{TRUE}\hlstd{)]}
\end{alltt}
\begin{verbatim}
## [1] ADAM9 <NA> AP2A2 <NA> <NA> BZW2 <NA>
## [8] CEP135 CLIP4 DPH5 EIF4E2 EMC1 ERO1LB EXOSC2
## [15] GGH GLA GOLGA7 HDAC2 HECTD1 HS6ST2 IDE
## [22] <NA> LARP1 LARP4B LARP7 <NA> MIPOL1 MOV10
## [29] MYCBP2 NAT14 NGLY1 NPC2 NUPL1 PITRM1 PLOD2
## [36] PMPCB POR PRKAR2A PTBP2 RAB14 RAB1A RAB2A
## [43] RAP1GDS1 RBX1 REEP6 RPL36 SCCPDH <NA> <NA>
## [50] TIMM8B TRIM59 TUBGCP2 <NA> <NA>
## 332 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACSL3 ADAM9 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
\end{document}