\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{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
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\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb
\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
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{\par\unskip\endMakeFramed%
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\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{Janvier 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle
\tableofcontents
\newpage
\section{Data}
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{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] 333 161
\end{verbatim}
\end{kframe}
\end{knitrout}
\section{Comparison of dataset}
\subsection{Data}
\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_BUSTED"}\hlstd{,} \hlstr{"bats_BppM1M2"}\hlstd{,} \hlstr{"bats_BppM7M8"}\hlstd{,}
\hlstr{"bats_codemlM1M2"}\hlstd{,} \hlstr{"bats_codemlM7M8"}\hlstd{,} \hlstr{"dginn.primate_codemlM1M2"}\hlstd{,}
\hlstr{"dginn.primate_codemlM7M8"}\hlstd{,} \hlstr{"dginn.primate_BppM1M2"}\hlstd{,}
\hlstr{"dginn.primate_BppM7M8"}\hlstd{,} \hlstr{"dginn.primate_BUSTED"}\hlstd{)])}
\hlkwd{dim}\hlstd{(tmp)}
\end{alltt}
\begin{verbatim}
## [1] 206 11
\end{verbatim}
\end{kframe}
\end{knitrout}
\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{(tmp}\hlopt{$}\hlstd{Gene.name)}
\hlstd{batstmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\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{primatetmp}\hlkwb{<-}\hlkwd{rowSums}\hlstd{(}\hlkwd{cbind}\hlstd{(tmp}\hlopt{$}\hlstr{"dginn.primate_codemlM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tmp}\hlopt{$}\hlstr{"dginn.primate_codemlM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BppM1M2"}\hlopt{==}\hlstr{"Y"}\hlstd{,}
\hlstd{tmp}\hlopt{$}\hlstr{"dginn.primate_BppM7M8"}\hlopt{==}\hlstr{"Y"}\hlstd{, tmp}\hlopt{$}\hlstr{"dginn.primate_BUSTED"}\hlopt{==}\hlstr{"Y"}\hlstd{))}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn3}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(primatetmp}\hlopt{>=}\hlnum{3}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{bats_dginn4}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(batstmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(primatetmp}\hlopt{>=}\hlnum{4}\hlstd{,} \hlnum{1}\hlstd{,}\hlnum{0}\hlstd{)}
\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{2}\hlopt{:}\hlnum{3}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN bats >3"}\hlstd{,} \hlstr{"DGINN primate >3"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianbats-1}
\begin{kframe}\begin{alltt}
\hlkwd{mondrian}\hlstd{(monddata[,}\hlnum{4}\hlopt{:}\hlnum{5}\hlstd{],} \hlkwc{labels}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"DGINN bats >4"}\hlstd{,} \hlstr{"DGINN primate >4"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/mondrianbats-2}
\end{knitrout}
\subsection{subsetR}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(UpSetR)}
\hlkwd{upset}\hlstd{(monddata,} \hlkwc{nsets} \hlstd{=} \hlnum{4}\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/subsetbats-1}
\begin{kframe}\begin{alltt}
\hlkwd{upset}\hlstd{(monddata[,}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{],} \hlkwc{nsets} \hlstd{=} \hlnum{2}\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/subsetbats-2}
\begin{kframe}\begin{alltt}
\hlkwd{upset}\hlstd{(monddata[,}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{4}\hlstd{,}\hlnum{5}\hlstd{)],} \hlkwc{nsets} \hlstd{=} \hlnum{2}\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/subsetbats-3}
\end{knitrout}
\section{Which are these genes?}
\subsection{Gene under positive selection in both bats and primates}
4 methods:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 4 ACADM 1 1 1 1
## 73 GGH 1 1 1 1
## 78 GOLGA7 1 1 1 1
## 89 IDE 1 1 1 1
## 94 ITGB1 1 1 1 1
## 97 LMAN2 1 1 1 1
## 132 POLA1 1 1 1 1
## 164 SLC27A2 1 1 1 1
## 188 TOR1AIP1 1 1 1 1
## 201 VPS39 1 1 1 1
\end{verbatim}
\end{kframe}
\end{knitrout}
3 methods:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 4 ACADM 1 1 1 1
## 20 CDK5RAP2 1 1 0 1
## 48 EDEM3 1 1 1 0
## 73 GGH 1 1 1 1
## 78 GOLGA7 1 1 1 1
## 89 IDE 1 1 1 1
## 94 ITGB1 1 1 1 1
## 97 LMAN2 1 1 1 1
## 104 MOV10 1 1 0 0
## 132 POLA1 1 1 1 1
## 164 SLC27A2 1 1 1 1
## 188 TOR1AIP1 1 1 1 1
## 201 VPS39 1 1 1 1
\end{verbatim}
\end{kframe}
\end{knitrout}
\subsection{Gene under positive selection only in primates}
4 methods:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 20 CDK5RAP2 1 1 0 1
## 23 CEP135 0 1 0 1
## 26 CEP68 0 1 0 1
## 32 CLIP4 0 1 0 1
## 45 DPH5 0 1 0 1
## 50 EMC1 0 1 0 1
## 68 FYCO1 0 1 0 1
## 74 GIGYF2 0 1 0 1
## 75 GLA 0 1 0 1
## 83 HECTD1 0 1 0 1
## 95 LARP1 0 1 0 1
## 108 MYCBP2 0 1 0 1
## 111 NDUFB9 0 1 0 1
## 138 PRKAR2A 0 1 0 1
## 153 RIPK1 0 1 0 1
## 156 SAAL1 0 1 0 1
## 160 SEPSECS 0 1 0 1
## 162 SIRT5 0 1 0 1
## 163 SLC25A21 0 1 0 1
## 185 TMEM39B 0 1 0 1
## 191 TUBGCP2 0 1 0 1
## 194 UBAP2 0 1 0 1
## 197 UGGT2 0 1 0 1
## 204 ZNF318 0 1 0 1
\end{verbatim}
\end{kframe}
\end{knitrout}
3 methods:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{1}\hlstd{,]}
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 23 CEP135 0 1 0 1
## 26 CEP68 0 1 0 1
## 32 CLIP4 0 1 0 1
## 33 CNTRL 0 1 0 0
## 45 DPH5 0 1 0 1
## 50 EMC1 0 1 0 1
## 56 EXOSC2 0 1 0 0
## 68 FYCO1 0 1 0 1
## 74 GIGYF2 0 1 0 1
## 75 GLA 0 1 0 1
## 79 GOLGB1 0 1 0 0
## 80 GORASP1 0 1 0 0
## 83 HECTD1 0 1 0 1
## 95 LARP1 0 1 0 1
## 96 LARP7 0 1 0 0
## 100 MDN1 0 1 0 0
## 107 MRPS5 0 1 0 0
## 108 MYCBP2 0 1 0 1
## 111 NDUFB9 0 1 0 1
## 115 NGLY1 0 1 0 0
## 118 NPC2 0 1 0 0
## 127 PITRM1 0 1 0 0
## 128 PLAT 0 1 0 0
## 134 POR 0 1 0 0
## 138 PRKAR2A 0 1 0 1
## 144 RAB14 0 1 0 0
## 145 RAB2A 0 1 0 0
## 153 RIPK1 0 1 0 1
## 156 SAAL1 0 1 0 1
## 160 SEPSECS 0 1 0 1
## 162 SIRT5 0 1 0 1
## 163 SLC25A21 0 1 0 1
## 172 STOM 0 1 0 0
## 181 TIMM8B 0 1 0 0
## 185 TMEM39B 0 1 0 1
## 189 TRIM59 0 1 0 0
## 190 TRMT1 0 1 0 0
## 191 TUBGCP2 0 1 0 1
## 194 UBAP2 0 1 0 1
## 197 UGGT2 0 1 0 1
## 199 USP54 0 1 0 0
## 204 ZNF318 0 1 0 1
\end{verbatim}
\end{kframe}
\end{knitrout}
\subsection{Gene under positive selection only in bats}
4 methods:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn4}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn4}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 48 EDEM3 1 1 1 0
## 52 ERGIC1 1 0 1 0
## 91 IMPDH2 1 0 1 0
## 92 INHBE 1 0 1 0
## 166 SLC44A2 1 0 1 0
## 177 TBK1 1 0 1 0
\end{verbatim}
\end{kframe}
\end{knitrout}
3 methods:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{monddata[monddata}\hlopt{$}\hlstd{bats_dginn3}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{monddata}\hlopt{$}\hlstd{primate_dginn3}\hlopt{==}\hlnum{0}\hlstd{,]}
\end{alltt}
\begin{verbatim}
## tmp$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 primate_dginn4
## 7 AGPS 1 0 0 0
## 52 ERGIC1 1 0 1 0
## 81 GRIPAP1 1 0 0 0
## 82 GRPEL1 1 0 0 0
## 91 IMPDH2 1 0 1 0
## 92 INHBE 1 0 1 0
## 120 NUP214 1 0 0 0
## 136 PRIM1 1 0 0 0
## 165 SLC30A9 1 0 0 0
## 166 SLC44A2 1 0 1 0
## 177 TBK1 1 0 1 0
\end{verbatim}
\end{kframe}
\end{knitrout}
\subsection{Figure tableau}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tablo}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tablo}\hlopt{$}\hlstd{nbats}\hlkwb{<-}\hlstd{batstmp}
\hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlkwb{<-}\hlstd{primatetmp}
\hlkwd{plot}\hlstd{(}\hlkwa{NULL}\hlstd{,} \hlkwc{xlim}\hlstd{=}\hlkwd{c}\hlstd{(}\hlopt{-}\hlnum{0.5}\hlstd{,}\hlnum{5.5}\hlstd{),} \hlkwc{ylim}\hlstd{=}\hlkwd{c}\hlstd{(}\hlopt{-}\hlnum{3}\hlstd{,}\hlnum{5.5}\hlstd{),} \hlkwc{xlab}\hlstd{=}\hlstr{"bats"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"primates"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Genes supported by x,y methods in bats and primates"}\hlstd{,} \hlkwc{bty}\hlstd{=}\hlstr{"n"}\hlstd{,} \hlkwc{xaxt}\hlstd{=}\hlstr{"n"}\hlstd{,} \hlkwc{yaxt}\hlstd{=}\hlstr{"n"}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwc{x}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlopt{-}\hlnum{0.6}\hlstd{,} \hlnum{6}\hlstd{),} \hlkwc{y}\hlstd{=}\hlnum{0}\hlopt{:}\hlnum{5}\hlstd{,} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwc{y}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlopt{-}\hlnum{0.65}\hlstd{,} \hlnum{6}\hlstd{),} \hlkwc{x}\hlstd{=}\hlnum{0}\hlopt{:}\hlnum{5}\hlstd{,} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)}
\hlkwd{sapply}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{by}\hlstd{=}\hlnum{1}\hlstd{),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)\{}
\hlkwd{segments}\hlstd{(}\hlkwc{x0}\hlstd{=x,} \hlkwc{x1}\hlstd{=x,} \hlkwc{y0}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{y1}\hlstd{=}\hlnum{5.5}\hlstd{)}
\hlstd{\})}
\end{alltt}
\begin{verbatim}
## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
## NULL
##
## [[6]]
## NULL
##
## [[7]]
## NULL
\end{verbatim}
\begin{alltt}
\hlkwd{sapply}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{by}\hlstd{=}\hlnum{1}\hlstd{),} \hlkwa{function}\hlstd{(}\hlkwc{x}\hlstd{)\{}
\hlkwd{segments}\hlstd{(}\hlkwc{x0}\hlstd{=}\hlopt{-}\hlnum{0.5}\hlstd{,} \hlkwc{x1}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{y0}\hlstd{=x,} \hlkwc{y1}\hlstd{=x)}
\hlstd{\})}
\end{alltt}
\begin{verbatim}
## [[1]]
## NULL
##
## [[2]]
## NULL
##
## [[3]]
## NULL
##
## [[4]]
## NULL
##
## [[5]]
## NULL
##
## [[6]]
## NULL
##
## [[7]]
## NULL
\end{verbatim}
\begin{alltt}
\hlkwa{for} \hlstd{(p} \hlkwa{in} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)\{}
\hlkwa{for} \hlstd{(b} \hlkwa{in} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)\{}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlstd{b} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlstd{p]}
\hlkwa{if}\hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{0} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<}\hlnum{8}\hlstd{)\{}
\hlkwd{text}\hlstd{(b,}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)), tmp,} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlstd{\}}\hlkwa{else if} \hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{8} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<}\hlnum{16}\hlstd{)\{}
\hlkwd{print}\hlstd{(}\hlkwd{c}\hlstd{(p, b))}
\hlkwd{text}\hlstd{((b}\hlopt{-}\hlnum{0.3}\hlstd{),}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{=} \hlnum{8}\hlstd{), tmp[}\hlnum{1}\hlopt{:}\hlnum{8}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{((b}\hlopt{+}\hlnum{0.3}\hlstd{),}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{= (}\hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{8}\hlstd{)), tmp[}\hlnum{9}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlstd{\}}\hlkwa{else if} \hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{16}\hlstd{)\{}
\hlkwd{text}\hlstd{(b,p,} \hlkwd{paste0}\hlstd{(}\hlkwd{length}\hlstd{(tmp),} \hlstr{" values"}\hlstd{))}
\hlstd{\}}
\hlstd{\}}
\hlstd{\}}
\end{alltt}
\begin{verbatim}
## [1] 0 1
## [1] 1 2
## [1] 2 0
## [1] 2 1
\end{verbatim}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{1}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{1.2}\hlstd{,} \hlstr{"p=1/n=0"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.1}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{3}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.3}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{1} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{1}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{1.7}\hlstd{,} \hlstr{"p=1/n=1"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.6}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{2}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{1.8}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
{\ttfamily\noindent\bfseries\color{errorcolor}{\#\# Error in seq.default(from = 0.1, to = 2, length.out = length(tmp) - 18): 'length.out' must be a non-negative number}}\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{0} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{0}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{2.2}\hlstd{,} \hlstr{"p=0/n=0"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{17}\hlstd{),}\hlopt{-}\hlnum{2.1}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{17}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{4.4}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{17}\hlstd{),}\hlopt{-}\hlnum{2.3}\hlstd{, tmp[}\hlnum{18}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{2} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{0}\hlstd{]}
\hlkwd{text}\hlstd{(}\hlopt{-}\hlnum{0.4}\hlstd{,}\hlopt{-}\hlnum{2.7}\hlstd{,} \hlstr{"p=0/n=2"}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.6}\hlstd{)}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{18}\hlstd{),}\hlopt{-}\hlnum{2.6}\hlstd{, tmp[}\hlnum{1}\hlopt{:}\hlnum{18}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/tablo-1}
\begin{kframe}\begin{alltt}
\hlkwd{text}\hlstd{(}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=}\hlnum{0.1}\hlstd{,} \hlkwc{to}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{2.8}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\end{alltt}
{\ttfamily\noindent\bfseries\color{errorcolor}{\#\# Error in seq.default(from = 0.1, to = 1, length.out = length(tmp) - 18): 'length.out' must be a non-negative number}}\end{kframe}
\end{knitrout}
\end{document}