\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{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} \end{kframe} \end{knitrout} \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_alldginn.txt"}\hlstd{),} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)} \hlkwd{dim}\hlstd{(tab)} \end{alltt} \begin{verbatim} ## [1] 442 55 \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] 323 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 ## 6 ACADM 1 1 1 ## 7 ACE2 1 1 1 ## 109 GGH 1 1 1 ## 117 GOLGA7 1 1 1 ## 134 IDE 1 1 1 ## 139 ITGB1 1 1 1 ## 146 LMAN2 1 1 1 ## 212 POLA1 1 1 1 ## 263 SLC27A2 1 1 1 ## 301 TOR1AIP1 1 1 1 ## 314 VPS39 1 1 1 ## primate_dginn4 ## 6 1 ## 7 1 ## 109 1 ## 117 1 ## 134 1 ## 139 1 ## 146 1 ## 212 1 ## 263 1 ## 301 1 ## 314 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$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 ## 6 ACADM 1 1 1 ## 7 ACE2 1 1 1 ## 9 ADAM9 1 1 0 ## 34 CDK5RAP2 1 1 0 ## 71 EDEM3 1 1 1 ## 109 GGH 1 1 1 ## 117 GOLGA7 1 1 1 ## 134 IDE 1 1 1 ## 139 ITGB1 1 1 1 ## 146 LMAN2 1 1 1 ## 157 MIPOL1 1 1 0 ## 159 MOV10 1 1 0 ## 212 POLA1 1 1 1 ## 239 RAP1GDS1 1 1 1 ## 257 SCCPDH 1 1 0 ## 263 SLC27A2 1 1 1 ## 301 TOR1AIP1 1 1 1 ## 314 VPS39 1 1 1 ## primate_dginn4 ## 6 1 ## 7 1 ## 9 0 ## 34 1 ## 71 0 ## 109 1 ## 117 1 ## 134 1 ## 139 1 ## 146 1 ## 157 1 ## 159 0 ## 212 1 ## 239 0 ## 257 0 ## 263 1 ## 301 1 ## 314 1 \end{verbatim} \end{kframe} \end{knitrout} \subsection{Gene under positive selection only in primates} 4 methods: \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{monddata[monddata}\hlopt{$}\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 ## 31 BRD4 0 1 0 ## 34 CDK5RAP2 1 1 0 ## 37 CEP135 0 1 0 ## 40 CEP68 0 1 0 ## 47 CLIP4 0 1 0 ## 67 DNMT1 0 1 0 ## 68 DPH5 0 1 0 ## 75 EMC1 0 1 0 ## 80 ERO1B 0 1 0 ## 101 FYCO1 0 1 0 ## 105 GCC2 0 1 0 ## 110 GHITM 0 1 0 ## 111 GIGYF2 0 1 0 ## 112 GLA 0 1 0 ## 127 HECTD1 0 1 0 ## 143 LARP1 0 1 0 ## 144 LARP4B 0 1 0 ## 150 MARK1 0 1 0 ## 157 MIPOL1 1 1 0 ## 160 MPHOSPH10 0 1 0 ## 166 MYCBP2 0 1 0 ## 171 NDUFAF2 0 1 0 ## 172 NDUFB9 0 1 0 ## 187 NUP58 0 1 0 ## 195 PCNT 0 1 0 ## 218 PRIM2 0 1 0 ## 220 PRKAR2A 0 1 0 ## 227 PVR 0 1 0 ## 245 REEP6 0 1 0 ## 248 RIPK1 0 1 0 ## 253 SAAL1 0 1 0 ## 259 SEPSECS 0 1 0 ## 261 SIRT5 0 1 0 ## 262 SLC25A21 0 1 0 ## 296 TMEM39B 0 1 0 ## 298 TMPRSS2 0 1 0 ## 304 TUBGCP2 0 1 0 ## 307 UBAP2 0 1 0 ## 310 UGGT2 0 1 0 ## 321 ZNF318 0 1 0 ## primate_dginn4 ## 31 1 ## 34 1 ## 37 1 ## 40 1 ## 47 1 ## 67 1 ## 68 1 ## 75 1 ## 80 1 ## 101 1 ## 105 1 ## 110 1 ## 111 1 ## 112 1 ## 127 1 ## 143 1 ## 144 1 ## 150 1 ## 157 1 ## 160 1 ## 166 1 ## 171 1 ## 172 1 ## 187 1 ## 195 1 ## 218 1 ## 220 1 ## 227 1 ## 245 1 ## 248 1 ## 253 1 ## 259 1 ## 261 1 ## 262 1 ## 296 1 ## 298 1 ## 304 1 ## 307 1 ## 310 1 ## 321 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 ## 19 AP2A2 0 1 0 ## 23 ATE1 0 1 0 ## 31 BRD4 0 1 0 ## 32 BZW2 0 1 0 ## 37 CEP135 0 1 0 ## 40 CEP68 0 1 0 ## 47 CLIP4 0 1 0 ## 48 CNTRL 0 1 0 ## 67 DNMT1 0 1 0 ## 68 DPH5 0 1 0 ## 72 EIF4E2 0 1 0 ## 75 EMC1 0 1 0 ## 80 ERO1B 0 1 0 ## 83 EXOSC2 0 1 0 ## 101 FYCO1 0 1 0 ## 105 GCC2 0 1 0 ## 110 GHITM 0 1 0 ## 111 GIGYF2 0 1 0 ## 112 GLA 0 1 0 ## 118 GOLGB1 0 1 0 ## 119 GORASP1 0 1 0 ## 125 HDAC2 0 1 0 ## 127 HECTD1 0 1 0 ## 131 HS6ST2 0 1 0 ## 143 LARP1 0 1 0 ## 144 LARP4B 0 1 0 ## 145 LARP7 0 1 0 ## 150 MARK1 0 1 0 ## 154 MDN1 0 1 0 ## 160 MPHOSPH10 0 1 0 ## 164 MRPS5 0 1 0 ## 166 MYCBP2 0 1 0 ## 168 NAT14 0 1 0 ## 171 NDUFAF2 0 1 0 ## 172 NDUFB9 0 1 0 ## 176 NGLY1 0 1 0 ## 181 NPC2 0 1 0 ## 187 NUP58 0 1 0 ## 195 PCNT 0 1 0 ## 202 PITRM1 0 1 0 ## 204 PLAT 0 1 0 ## 208 PLOD2 0 1 0 ## 210 PMPCB 0 1 0 ## 214 POR 0 1 0 ## 218 PRIM2 0 1 0 ## 220 PRKAR2A 0 1 0 ## 224 PTBP2 0 1 0 ## 227 PVR 0 1 0 ## 230 RAB14 0 1 0 ## 232 RAB1A 0 1 0 ## 233 RAB2A 0 1 0 ## 242 RBX1 0 1 0 ## 245 REEP6 0 1 0 ## 248 RIPK1 0 1 0 ## 250 RPL36 0 1 0 ## 253 SAAL1 0 1 0 ## 259 SEPSECS 0 1 0 ## 261 SIRT5 0 1 0 ## 262 SLC25A21 0 1 0 ## 277 STOM 0 1 0 ## 290 TIMM8B 0 1 0 ## 296 TMEM39B 0 1 0 ## 298 TMPRSS2 0 1 0 ## 302 TRIM59 0 1 0 ## 303 TRMT1 0 1 0 ## 304 TUBGCP2 0 1 0 ## 307 UBAP2 0 1 0 ## 310 UGGT2 0 1 0 ## 312 USP54 0 1 0 ## 321 ZNF318 0 1 0 ## primate_dginn4 ## 19 0 ## 23 0 ## 31 1 ## 32 0 ## 37 1 ## 40 1 ## 47 1 ## 48 0 ## 67 1 ## 68 1 ## 72 0 ## 75 1 ## 80 1 ## 83 0 ## 101 1 ## 105 1 ## 110 1 ## 111 1 ## 112 1 ## 118 0 ## 119 0 ## 125 0 ## 127 1 ## 131 0 ## 143 1 ## 144 1 ## 145 0 ## 150 1 ## 154 0 ## 160 1 ## 164 0 ## 166 1 ## 168 0 ## 171 1 ## 172 1 ## 176 0 ## 181 0 ## 187 1 ## 195 1 ## 202 0 ## 204 0 ## 208 0 ## 210 0 ## 214 0 ## 218 1 ## 220 1 ## 224 0 ## 227 1 ## 230 0 ## 232 0 ## 233 0 ## 242 0 ## 245 1 ## 248 1 ## 250 0 ## 253 1 ## 259 1 ## 261 1 ## 262 1 ## 277 0 ## 290 0 ## 296 1 ## 298 1 ## 302 0 ## 303 0 ## 304 1 ## 307 1 ## 310 1 ## 312 0 ## 321 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 ## 14 AKAP9 1 0 1 ## 26 ATP6AP1 1 0 1 ## 44 CISD3 1 0 1 ## 71 EDEM3 1 1 1 ## 77 ERGIC1 1 0 1 ## 136 IMPDH2 1 0 1 ## 137 INHBE 1 0 1 ## 231 RAB18 1 0 1 ## 239 RAP1GDS1 1 1 1 ## 267 SLC44A2 1 0 1 ## 283 TBK1 1 0 1 ## primate_dginn4 ## 14 0 ## 26 0 ## 44 0 ## 71 0 ## 77 0 ## 136 0 ## 137 0 ## 231 0 ## 239 0 ## 267 0 ## 283 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$Gene.name bats_dginn3 primate_dginn3 bats_dginn4 ## 5 ACAD9 1 0 0 ## 11 AGPS 1 0 0 ## 14 AKAP9 1 0 1 ## 26 ATP6AP1 1 0 1 ## 44 CISD3 1 0 1 ## 49 COL6A1 1 0 0 ## 77 ERGIC1 1 0 1 ## 122 GRIPAP1 1 0 0 ## 123 GRPEL1 1 0 0 ## 136 IMPDH2 1 0 1 ## 137 INHBE 1 0 1 ## 151 MARK2 1 0 0 ## 185 NUP214 1 0 0 ## 217 PRIM1 1 0 0 ## 226 PUSL1 1 0 0 ## 231 RAB18 1 0 1 ## 266 SLC30A9 1 0 0 ## 267 SLC44A2 1 0 1 ## 268 SLC9A3R1 1 0 0 ## 283 TBK1 1 0 1 ## primate_dginn4 ## 5 0 ## 11 0 ## 14 0 ## 26 0 ## 44 0 ## 49 0 ## 77 0 ## 122 0 ## 123 0 ## 136 0 ## 137 0 ## 151 0 ## 185 0 ## 217 0 ## 226 0 ## 231 0 ## 266 0 ## 267 0 ## 268 0 ## 283 0 \end{verbatim} \end{kframe} \end{knitrout} \subsection{Figure tableau} \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlstd{tablo}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(tmp}\hlopt{$}\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] 1 2 ## [1] 2 0 ## [1] 2 1 ## [1] 2 2 ## [1] 3 0 ## [1] 3 1 ## [1] 4 0 ## [1] 4 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{5.5}\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{4.5}\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{)} \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{2.3}\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{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlnum{17}\hlstd{),}\hlopt{-}\hlnum{2.3}\hlstd{, tmp[}\hlnum{18}\hlopt{:}\hlnum{34}\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{5.5}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{34}\hlstd{),}\hlopt{-}\hlnum{2.5}\hlstd{, tmp[}\hlnum{35}\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{2.9}\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{2.8}\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{1}\hlstd{,} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{18}\hlstd{),}\hlopt{-}\hlnum{3.0}\hlstd{, tmp[}\hlnum{19}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)} \end{alltt} \end{kframe} \includegraphics[width=\maxwidth]{figure/tablo-1} \end{knitrout} \begin{knitrout} \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe} \begin{alltt} \hlkwd{write.csv}\hlstd{(tablo[tablo}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{,}\hlstr{"tmp$Gene.name"}\hlstd{],} \hlstr{"batssup3.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)} \hlkwd{write.csv}\hlstd{(tablo[tablo}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{,}\hlstr{"tmp$Gene.name"}\hlstd{],} \hlstr{"primatessup3.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)} \hlkwd{write.csv}\hlstd{(tablo,} \hlstr{"primatesVbats.csv"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{)} \end{alltt} \end{kframe} \end{knitrout} \end{document}