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  • mcariou/2020_dginn_covid19
  • ciri/ps_sars-cov-2/2021_dginn_covid19
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covid_comp_dataset.Rnw
View file @ 77f559a1
......@@ -313,7 +313,7 @@ write.csv(tabloK, "primatesVbats_onlykrogan.csv", row.names=FALSE, quote=FALSE)
\section{Tanglegram}
<<eval=FALSE>>=
<<eval=TRUE>>=
#install.packages('dendextend') # stable CRAN version
library(dendextend) # load the package
#install.packages("phytools") # stable CRAN version
......@@ -322,15 +322,13 @@ library(ggraph)
library(igraph)
library(tidyverse)
##
tmp<-tablo[(tablo$nbats!=0 | tablo$nprimates!=0),]
tmp<-head(tablo, 20)
#tmp<-head(tablo, 20)
#tmp<-rbind(as.matrix(tmp), c("outgroup", 50, 50))
tmp<-as.data.frame(tmp)
matbats<-hclust(dist(tmp$nbats))
matpri<-hclust(dist(tmp$nprimates))
tmp[order(tmp$nbats),]
dendpri<-as.dendrogram(matpri)
......@@ -347,14 +345,11 @@ tmp[order(tmp$nbats, decreasing=FALSE),]$'tmp$Gene.name'-> order
dendbats<-dendextend::rotate(dendbats, order=order)
#### Il faut swapper certains neud de l'arbrese
class(labels(dendpri))
dend12 <- dendlist(dendbats, dendpri)
?png
png("tanglegramm.png", width = 1800, height = 3000)
png("figure/tanglegramm.png", width = 1800, height = 3000)
tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
edge.lwd=0, margin_inner=6,
margin_top=2,
......@@ -367,12 +362,151 @@ tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
dev.off()
tmp
?tanglegram
@
<<eval=TRUE>>=
ace<-264
tmprss2<-75
znf318<-81
sepsecs<-228
tbk1<-273
ripk1<-224
col<-rep("grey", length(labels(dendpri)))
col[ace]<-"black"
col[tmprss2]<-"black"
col[znf318]<-"black"
col[sepsecs]<-"black"
col[tbk1]<-"black"
col[ripk1]<-"black"
font<-rep(1, length(labels(dendpri))*2)
#font[ace]<-1.3
#font[tmprss2]<-1.3
#font[length(labels(dendpri))+160]<-1.3
png("figure/tanglegramm.png", width = 1800, height = 3000)
tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
edge.lwd=0, margin_inner=6,
margin_top=2,
main_left=" bats",
main_right = "primates ",
lwd=0.5,
cex_main=1,
lab.cex=font,
k_labels=6,
color_lines=col)
dev.off()
@
<<>>=
tmp<-tablo[(tablo$nbats>=3 | tablo$nprimates>=3),]
dim(tmp)
tmp<-as.data.frame(tmp)
names(tmp)<-c("tmp.Gene.name", "nbats", "nprimates")
matbats<-hclust(dist(tmp$nbats))
matpri<-hclust(dist(tmp$nprimates))
#tmp[order(tmp$nbats),]
dendpri<-as.dendrogram(matpri)
dendbats<-as.dendrogram(matbats)
labels(dendpri)<-as.character(tmp$tmp.Gene.name[labels(dendpri)])
labels(dendbats)<-as.character(tmp$tmp.Gene.name[labels(dendbats)])
tmp[order(tmp$nprimates, decreasing=FALSE),]$tmp.Gene.name-> order
dendpri<-dendextend::rotate(dendpri, order=order)
tmp[order(tmp$nbats, decreasing=FALSE),]$tmp.Gene.name-> order
dendbats<-dendextend::rotate(dendbats, order=order)
#### Il faut swapper certains neuds de l'arbres
class(labels(dendpri))
dend12 <- dendlist(dendbats, dendpri)
ace<-97
tmprss2<-27
znf318<-31
sepsecs<-69
tbk1<-106
ripk1<-68
col<-rep("lightblue", length(labels(dendpri)))
plusplus<-tmp$tmp.Gene.name[tmp$nbats>=3 & tmp$nprimates>=3]
col[which(labels(dendbats) %in% plusplus)]<-"pink"
interest<-c("TMPRSS2","ZNF318", "SEPSECS","TBK1", "RIPK1")
col[which(labels(dendbats) %in% interest)]<-"blue"
interestpp<-c("ACE2")
col[which(labels(dendbats) %in% interestpp)]<-"red"
png("figure/tanglegrammsup3.png", width = 500, height = 1200)
tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
edge.lwd=0, margin_inner=6,
margin_top=3,
main_left=" bats",
main_right = "primates ",
lwd=0.5,
cex_main=2,
lab.cex=1,
k_labels=6,
color_lines=col)
dev.off()
### Changer couleurs des groupes
## changer couleurs des lines sel vs sel or sel vs non-sel
setEPS()
postscript("figure/tanglegramsup3.eps", height=15, width=5)
tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
edge.lwd=0, margin_inner=6,
margin_top=3,
main_left=" bats",
main_right = "primates ",
lwd=0.5,
cex_main=2,
lab.cex=1,
# k_labels=6,
color_lines=col)
dev.off()
labels_colors(dend12[[1]])<-rep(rainbow(15)[c(1:3, 9:11)], table(tmp$nbats))
labels_colors(dend12[[2]])<-rep(rainbow(15)[c(1:3, 9:11)], table(tmp$nprimates))
labels_colors(dend12[[1]])<-rep(viridis(10)[c(1:3, 7:9)], table(tmp$nbats))
labels_colors(dend12[[2]])<-rep(viridis(10)[c(1:3, 7:9)], table(tmp$nprimates))
setEPS()
postscript("figure/tanglegramsup3_V2.eps", height=15, width=5)
tanglegram(dend12, columns_width=c(3, 3,3), axes=FALSE,
edge.lwd=0, margin_inner=6,
margin_top=3,
main_left=" bats",
main_right = "primates ",
lwd=0.5,
cex_main=2,
lab.cex=1,
# k_labels=6,
color_lines=col)
dev.off()
@
\end{document}
......
covid_comp_dataset.log deleted 100644 → 0
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This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2021.2.23) 26 FEB 2021 17:33
entering extended mode
restricted \write18 enabled.
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**covid_comp_dataset.tex
(./covid_comp_dataset.tex
LaTeX2e <2017-04-15>
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Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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File: size11.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
)
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Package: graphicx 2017/06/01 v1.1a Enhanced LaTeX Graphics (DPC,SPQR)
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Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
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Package graphics Info: Driver file: pdftex.def on input line 99.
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Package color Info: Driver file: pdftex.def on input line 147.
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! LaTeX Error: File `framed.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Enter file name:
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<read *>
l.27 \makeatletter
^^M
Here is how much of TeX's memory you used:
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! ==> Fatal error occurred, no output PDF file produced!
covid_comp_dataset.pdf
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covid_comp_dataset.tex
View file @ 77f559a1
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covid_comp_maic-pancorona.Rnw 0 → 100644
View file @ 77f559a1
\documentclass[11pt, oneside]{article} % 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, maic}
\author{Marie Cariou}
\date{March 2021} % Activate to display a given date or no date
\begin{document}
\maketitle
\tableofcontents
\newpage
\section{Data}
output from covid\_comp\_dataset.
<<>>=
tablo<-read.table("primatesVbats.csv",
h=T, sep=",")
@
Output MAIC formatted by Léa. This table includes the DGINN "score".
<<>>=
home<-"/home/adminmarie/Documents/"
workdir<-paste0(home, "CIRI_BIBS_projects/2020_05_Etienne_covid/")
maic<-read.table(paste0(workdir, "data/covid_comp_maic.txt"),
h=T)
@
\section{MAIC}
\subsection{Boxplot}
<<boxplot, fig.height=12>>=
par(mfrow=c(2,1))
boxplot(maic$rank~maic$nbats, notch=TRUE, varwidth=TRUE, xlab="score DGINN", ylab="rank MAIC", main="Bats")
stripchart(maic$rank~maic$nbats, method="jitter", vertical=TRUE, pch=1, cex=0.3, add=TRUE)
boxplot(maic$rank~maic$nprimates, notch=TRUE, xlab="score DGINN", ylab="rank MAIC", main="Primates")
stripchart(maic$rank~maic$nprimates, method="jitter", vertical=TRUE, pch=1, cex=0.3, add=TRUE)
@
\subsection{Dotchart}
<<dotbats, fig.height=8>>=
tmp<-maic[maic$nbats>=3, c("gene", "rank", "nbats")]
tmp<-tmp[order(tmp$rank, decreasing = TRUE),]
tmp$col<-"black"
tmp$col[tmp$gene=="ACE2"]<-"red"
tmp$col[tmp$gene=="TMPRSS2"]<-"red"
tmp$pch[tmp$nbats==5]<-1
tmp$pch[tmp$nbats==4]<-20
tmp$pch[tmp$nbats==3]<-4
dotchart(tmp$rank, main="Bats DGINN >=3", xlab="rank MAIC", labels=tmp$gene, pch=tmp$pch, col=tmp$col)
legend("topright", c("5 (score DGINN)", "4", "3"), pch=c(1,20,4))
@
<<dotprimates, fig.height=12>>=
tmp<-maic[maic$nprimates>=3, c("gene", "rank", "nprimates")]
tmp<-tmp[order(tmp$rank, decreasing = TRUE),]
tmp$pch[tmp$nprimates==5]<-1
tmp$pch[tmp$nprimates==4]<-20
tmp$pch[tmp$nprimates==3]<-4
tmp$col<-"black"
tmp$col[tmp$gene=="ACE2"]<-"red"
tmp$col[tmp$gene=="TMPRSS2"]<-"red"
dotchart(tmp$rank, main="Primates DGINN >=3", xlab="rank MAIC", labels=tmp$gene, pch=tmp$pch, cex=0.8, col=tmp$col)
legend("topright", c("5 (score DGINN)", "4", "3"), pch=c(1,20,4))
@
\section{Pan Corona}
<<>>=
pancorona<-read.table(paste0(workdir, "data/pancorona_S5.csv"),
h=T, fill = TRUE, sep="\t")
names(pancorona)<-c("tmp.Gene.name", names(pancorona)[-1])
# Genes en commun
pancorona$tmp.Gene.name[pancorona$tmp.Gene.name %in% tablo$tmp.Gene.name]
# Uniquement dans le tableau pancorona
sort(pancorona$tmp.Gene.name[(pancorona$tmp.Gene.name %in% tablo$tmp.Gene.name)==FALSE])
## Uniquement dans tableau
sort(tablo$tmp.Gene.name[(tablo$tmp.Gene.name %in% pancorona$tmp.Gene.name)==FALSE])
@
<<pancorona, fig.height=8>>=
pancorona<-pancorona[,c("tmp.Gene.name", "TOTAL")]
pandginn<-na.omit(merge(pancorona, tablo, by="tmp.Gene.name", all.x=TRUE))
pandginn<-pandginn[order(pandginn$nprimates),]
pandginn<-pandginn[order(pandginn$TOTAL),]
dotchart(as.matrix(pandginn[,2]), labels = pandginn$tmp.Gene.name, xlim=c(0,5))
points(pandginn[,4], 1:nrow(pandginn), col="blue", pch=20, cex=0.7)
points(pandginn[,3], 1:nrow(pandginn), col="blue", pch=4)
legend("bottomright", c("pancorona score", "dginn primate score", "dginn bats score"), pch=c(1,20,4), col=c("black", "blue", "blue"))
@
A-t-on un enrichissement en Pan-corona dans nos gènes sous PS?
<<>>=
pandginnall<-merge(pancorona, tablo, by="tmp.Gene.name", all.x=FALSE,all.y=TRUE)
dim(pandginnall)
# test indépendance: under PS / in the pancorona list
table(is.na(pandginnall$TOTAL)==FALSE)
table(pandginnall$nbats>=3)
chi<-table(is.na(pandginnall$TOTAL)==FALSE,pandginnall$nbats>=3)
chi
chisq.test(chi)
table(is.na(pandginnall$TOTAL)==FALSE)
table(pandginnall$nprimates>=3)
chi<-table(is.na(pandginnall$TOTAL)==FALSE,pandginnall$nprimates>=3)
chi
chisq.test(chi)
@
No enrichment in PanCORONA in our genes under PS.
\end{document}
covid_comp_maic-pancorona.pdf 0 → 100644
View file @ 77f559a1
File added
covid_comp_maic-pancorona.tex 0 → 100644
View file @ 77f559a1
\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, maic}
\author{Marie Cariou}
\date{March 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle
\tableofcontents
\newpage
\section{Data}
output from covid\_comp\_dataset.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tablo}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlstr{"primatesVbats.csv"}\hlstd{,}
\hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
Output MAIC formatted by Léa. This table includes the DGINN "score".
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{home}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/"}
\hlstd{workdir}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"CIRI_BIBS_projects/2020_05_Etienne_covid/"}\hlstd{)}
\hlstd{maic}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{"data/covid_comp_maic.txt"}\hlstd{),}
\hlkwc{h}\hlstd{=T)}
\end{alltt}
\end{kframe}
\end{knitrout}
\section{MAIC}
\subsection{Boxplot}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{par}\hlstd{(}\hlkwc{mfrow}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{2}\hlstd{,}\hlnum{1}\hlstd{))}
\hlkwd{boxplot}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nbats,} \hlkwc{notch}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{varwidth}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"score DGINN"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Bats"}\hlstd{)}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning in bxp(list(stats = structure(c(21, 825, 1664, 2860, 5392, 15, 625.5, : some notches went outside hinges ('box'): maybe set notch=FALSE}}\begin{alltt}
\hlkwd{stripchart}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nbats,} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{vertical}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.3}\hlstd{,} \hlkwc{add}\hlstd{=}\hlnum{TRUE}\hlstd{)}
\hlkwd{boxplot}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nprimates,} \hlkwc{notch}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"score DGINN"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Primates"}\hlstd{)}
\hlkwd{stripchart}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nprimates,} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{vertical}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.3}\hlstd{,} \hlkwc{add}\hlstd{=}\hlnum{TRUE}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/boxplot-1}
\end{knitrout}
\subsection{Dotchart}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{maic[maic}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"gene"}\hlstd{,} \hlstr{"rank"}\hlstd{,} \hlstr{"nbats"}\hlstd{)]}
\hlstd{tmp}\hlkwb{<-}\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{decreasing} \hlstd{=} \hlnum{TRUE}\hlstd{),]}
\hlstd{tmp}\hlopt{$}\hlstd{col}\hlkwb{<-}\hlstr{"black"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"ACE2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{5}\hlstd{]}\hlkwb{<-}\hlnum{1}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlnum{20}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{3}\hlstd{]}\hlkwb{<-}\hlnum{4}
\hlkwd{dotchart}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{main}\hlstd{=}\hlstr{"Bats DGINN >=3"}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{labels}\hlstd{=tmp}\hlopt{$}\hlstd{gene,} \hlkwc{pch}\hlstd{=tmp}\hlopt{$}\hlstd{pch,} \hlkwc{col}\hlstd{=tmp}\hlopt{$}\hlstd{col)}
\hlkwd{legend}\hlstd{(}\hlstr{"topright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"5 (score DGINN)"}\hlstd{,} \hlstr{"4"}\hlstd{,} \hlstr{"3"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/dotbats-1}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{maic[maic}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"gene"}\hlstd{,} \hlstr{"rank"}\hlstd{,} \hlstr{"nprimates"}\hlstd{)]}
\hlstd{tmp}\hlkwb{<-}\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{decreasing} \hlstd{=} \hlnum{TRUE}\hlstd{),]}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{5}\hlstd{]}\hlkwb{<-}\hlnum{1}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlnum{20}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{3}\hlstd{]}\hlkwb{<-}\hlnum{4}
\hlstd{tmp}\hlopt{$}\hlstd{col}\hlkwb{<-}\hlstr{"black"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"ACE2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlkwd{dotchart}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{main}\hlstd{=}\hlstr{"Primates DGINN >=3"}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{labels}\hlstd{=tmp}\hlopt{$}\hlstd{gene,} \hlkwc{pch}\hlstd{=tmp}\hlopt{$}\hlstd{pch,} \hlkwc{cex}\hlstd{=}\hlnum{0.8}\hlstd{,} \hlkwc{col}\hlstd{=tmp}\hlopt{$}\hlstd{col)}
\hlkwd{legend}\hlstd{(}\hlstr{"topright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"5 (score DGINN)"}\hlstd{,} \hlstr{"4"}\hlstd{,} \hlstr{"3"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/dotprimates-1}
\end{knitrout}
\section{Pan Corona}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{pancorona}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{"data/pancorona_S5.csv"}\hlstd{),}
\hlkwc{h}\hlstd{=T,} \hlkwc{fill} \hlstd{=} \hlnum{TRUE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\hlkwd{names}\hlstd{(pancorona)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlkwd{names}\hlstd{(pancorona)[}\hlopt{-}\hlnum{1}\hlstd{])}
\hlcom{# Genes en commun}
\hlstd{pancorona}\hlopt{$}\hlstd{tmp.Gene.name[pancorona}\hlopt{$}\hlstd{tmp.Gene.name} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{tmp.Gene.name]}
\end{alltt}
\begin{verbatim}
## [1] TBK1 MARK3 GIGYF2 MARK2 G3BP1 LARP1 ACE2 PABPC1
## [9] TMPRSS2 AP3B1 CLCC1 CSDE1 HECTD1 MARK1 MEPCE PDE4DIP
## [17] POR PRKAR2B RAB5C RTN4 SRP54 UBAP2 UBAP2L UBXN8
## [25] SPART BZW2 EIF4E2 SMOC1 STOML2 DDX21 FAM98A G3BP2
## [33] MOV10 PABPC4 UPF1
## 105 Levels: ACE2 ANPEP AP3B1 ATXN2L BTF3 BZW2 CKAP5 CLCC1 ... YTHDF2
\end{verbatim}
\begin{alltt}
\hlcom{# Uniquement dans le tableau pancorona}
\hlkwd{sort}\hlstd{(pancorona}\hlopt{$}\hlstd{tmp.Gene.name[(pancorona}\hlopt{$}\hlstd{tmp.Gene.name} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{tmp.Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
\end{alltt}
\begin{verbatim}
## [1] ANPEP ATXN2L BTF3 CKAP5 CTSB CTSL
## [7] CYB5R3 DDX1 DDX5 DDX58 DHX9 DNM1L
## [13] EEF1A1 EIF2A EIF3F EIF4B EZR FLNA
## [19] FURIN FUS GSK3A GSK3B HDLBP HNRNPA1
## [25] HNRNPD HNRNPF HNRNPU IFIH1 IGF2BP1 IKBKB
## [31] IKBKE IRF3 ISG15 KPNA3 KPNB1 MYH9
## [37] NCL POLD1 POLR2B PRKRA RBM14 RCHY1
## [43] RPL13A RPL26 RPS13 RPS17 RPS19 RPS9
## [49] SDCBP SERBP1 SGTA SLC1A5 SNAP47 SSB
## [55] STING1 SYNCRIP TANC1 TBCB TMPRSS11D TRAF3
## [61] TUBA4A TUBB2A TUBB4A TUBB6 USP10 VPS36
## [67] XRCC5 XRCC6 YBX1 YTHDF2
## 105 Levels: ACE2 ANPEP AP3B1 ATXN2L BTF3 BZW2 CKAP5 CLCC1 ... YTHDF2
\end{verbatim}
\begin{alltt}
\hlcom{## Uniquement dans tableau }
\hlkwd{sort}\hlstd{(tablo}\hlopt{$}\hlstd{tmp.Gene.name[(tablo}\hlopt{$}\hlstd{tmp.Gene.name} \hlopt{%in%} \hlstd{pancorona}\hlopt{$}\hlstd{tmp.Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
\end{alltt}
\begin{verbatim}
## [1] AAR2 AASS AATF ABCC1 ACAD9 ACADM
## [7] ACSL3 ADAM9 ADAMTS1 AGPS AKAP8 AKAP8L
## [13] AKAP9 ALG11 ALG5 ALG8 ANO6 AP2A2
## [19] AP2M1 ARF6 ATE1 ATP13A3 ATP1B1 ATP6AP1
## [25] ATP6V1A BAG5 BCKDK BRD2 BRD4 CCDC86
## [31] CDK5RAP2 CENPF CEP112 CEP135 CEP250 CEP350
## [37] CEP68 CHMP2A CHPF CHPF2 CISD3 CIT
## [43] CLIP4 CNTRL COL6A1 COLGALT1 COMT COQ8B
## [49] CRTC3 CSNK2A2 CSNK2B CUL2 CWC27 CYB5B
## [55] DCAF7 DCAKD DCTPP1 DDX10 DNAJC11 DNAJC19
## [61] DNMT1 DPH5 DPY19L1 ECSIT EDEM3 EIF4H
## [67] ELOC EMC1 ERC1 ERGIC1 ERLEC1 ERMP1
## [73] ERO1B ERP44 ETFA EXOSC2 EXOSC3 EXOSC5
## [79] EXOSC8 F2RL1 FAM162A FAM8A1 FAR2 FASTKD5
## [85] FBLN5 FBN1 FBN2 FBXL12 FKBP10 FKBP15
## [91] FKBP7 FOXRED2 FYCO1 GCC1 GCC2 GDF15
## [97] GFER GGCX GGH GHITM GLA GNB1
## [103] GNG5 GOLGA2 GOLGA3 GOLGA7 GOLGB1 GORASP1
## [109] GPAA1 GPX1 GRIPAP1 GRPEL1 GTF2F2 HDAC2
## [115] HEATR3 HMOX1 HOOK1 HS2ST1 HS6ST2 HSBP1
## [121] HYOU1 IDE IL17RA IMPDH2 INHBE INTS4
## [127] ITGB1 JAKMIP1 KDELC1 KDELC2 LARP4B LARP7
## [133] LMAN2 LOX MAP7D1 MARC1 MAT2B MDN1
## [139] MIB1 MIPOL1 MOGS MPHOSPH10 MRPS2 MRPS25
## [145] MRPS27 MRPS5 MTCH1 MYCBP2 NARS2 NAT14
## [151] NDFIP2 NDUFAF1 NDUFAF2 NDUFB9 NEK9 NEU1
## [157] NGDN NGLY1 NIN NINL NLRX1 NOL10
## [163] NPC2 NPTX1 NSD2 NUP210 NUP214 NUP54
## [169] NUP58 NUP62 NUP88 NUP98 NUTF2 OS9
## [175] PCNT PCSK5 PCSK6 PDZD11 PIGO PIGS
## [181] PITRM1 PKP2 PLAT PLD3 PLEKHA5 PLEKHF2
## [187] PLOD2 PMPCA PMPCB POFUT1 POLA1 POLA2
## [193] PPIL3 PPT1 PRIM1 PRIM2 PRKACA PRKAR2A
## [199] PRRC2B PSMD8 PTBP2 PTGES2 PUSL1 PVR
## [205] QSOX2 RAB10 RAB14 RAB18 RAB1A RAB2A
## [211] RAB7A RAB8A RAE1 RALA RAP1GDS1 RBM28
## [217] RBM41 RBX1 RDX REEP5 REEP6 RETREG3
## [223] RHOA RIPK1 RNF41 RPL36 RRP9 SAAL1
## [229] SBNO1 SCAP SCARB1 SCCPDH SDF2 SELENOS
## [235] SEPSECS SIL1 SIRT5 SLC25A21 SLC27A2 SLC30A6
## [241] SLC30A7 SLC30A9 SLC44A2 SLC9A3R1 SLU7 SNIP1
## [247] SRP19 SRP72 STC2 STOM SUN2 TAPT1
## [253] TARS2 TBCA TBKBP1 TCF12 THTPA TIMM10
## [259] TIMM10B TIMM29 TIMM8B TIMM9 TLE1 TLE3
## [265] TM2D3 TMED5 TMEM39B TMEM97 TOMM70 TOR1A
## [271] TOR1AIP1 TRIM59 TRMT1 TUBGCP2 TUBGCP3 TYSND1
## [277] UGGT2 USP54 VPS11 VPS39 WASHC4 WFS1
## [283] YIF1A ZC3H18 ZC3H7A ZDHHC5 ZNF318 ZNF503
## [289] ZYG11B
## 324 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{pancorona}\hlkwb{<-}\hlstd{pancorona[,}\hlkwd{c}\hlstd{(}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlstr{"TOTAL"}\hlstd{)]}
\hlstd{pandginn}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(}\hlkwd{merge}\hlstd{(pancorona, tablo,} \hlkwc{by}\hlstd{=}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=}\hlnum{TRUE}\hlstd{))}
\hlstd{pandginn}\hlkwb{<-}\hlstd{pandginn[}\hlkwd{order}\hlstd{(pandginn}\hlopt{$}\hlstd{nprimates),]}
\hlstd{pandginn}\hlkwb{<-}\hlstd{pandginn[}\hlkwd{order}\hlstd{(pandginn}\hlopt{$}\hlstd{TOTAL),]}
\hlkwd{dotchart}\hlstd{(}\hlkwd{as.matrix}\hlstd{(pandginn[,}\hlnum{2}\hlstd{]),} \hlkwc{labels} \hlstd{= pandginn}\hlopt{$}\hlstd{tmp.Gene.name,} \hlkwc{xlim}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{5}\hlstd{))}
\hlkwd{points}\hlstd{(pandginn[,}\hlnum{4}\hlstd{],} \hlnum{1}\hlopt{:}\hlkwd{nrow}\hlstd{(pandginn),} \hlkwc{col}\hlstd{=}\hlstr{"blue"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.7}\hlstd{)}
\hlkwd{points}\hlstd{(pandginn[,}\hlnum{3}\hlstd{],} \hlnum{1}\hlopt{:}\hlkwd{nrow}\hlstd{(pandginn),} \hlkwc{col}\hlstd{=}\hlstr{"blue"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{4}\hlstd{)}
\hlkwd{legend}\hlstd{(}\hlstr{"bottomright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"pancorona score"}\hlstd{,} \hlstr{"dginn primate score"}\hlstd{,} \hlstr{"dginn bats score"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{),} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"black"}\hlstd{,} \hlstr{"blue"}\hlstd{,} \hlstr{"blue"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/pancorona-1}
\end{knitrout}
A-t-on un enrichissement en Pan-corona dans nos gènes sous PS?
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{pandginnall}\hlkwb{<-}\hlkwd{merge}\hlstd{(pancorona, tablo,} \hlkwc{by}\hlstd{=}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=}\hlnum{FALSE}\hlstd{,}\hlkwc{all.y}\hlstd{=}\hlnum{TRUE}\hlstd{)}
\hlkwd{dim}\hlstd{(pandginnall)}
\end{alltt}
\begin{verbatim}
## [1] 324 4
\end{verbatim}
\begin{alltt}
\hlcom{# test indépendance: under PS / in the pancorona list}
\hlkwd{table}\hlstd{(}\hlkwd{is.na}\hlstd{(pandginnall}\hlopt{$}\hlstd{TOTAL)}\hlopt{==}\hlnum{FALSE}\hlstd{)}
\end{alltt}
\begin{verbatim}
##
## FALSE TRUE
## 289 35
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(pandginnall}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{)}
\end{alltt}
\begin{verbatim}
##
## FALSE TRUE
## 286 38
\end{verbatim}
\begin{alltt}
\hlstd{chi}\hlkwb{<-}\hlkwd{table}\hlstd{(}\hlkwd{is.na}\hlstd{(pandginnall}\hlopt{$}\hlstd{TOTAL)}\hlopt{==}\hlnum{FALSE}\hlstd{,pandginnall}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{)}
\hlstd{chi}
\end{alltt}
\begin{verbatim}
##
## FALSE TRUE
## FALSE 255 34
## TRUE 31 4
\end{verbatim}
\begin{alltt}
\hlkwd{chisq.test}\hlstd{(chi)}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning in chisq.test(chi): Chi-squared approximation may be incorrect}}\begin{verbatim}
##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: chi
## X-squared = 7.6869e-31, df = 1, p-value = 1
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(}\hlkwd{is.na}\hlstd{(pandginnall}\hlopt{$}\hlstd{TOTAL)}\hlopt{==}\hlnum{FALSE}\hlstd{)}
\end{alltt}
\begin{verbatim}
##
## FALSE TRUE
## 289 35
\end{verbatim}
\begin{alltt}
\hlkwd{table}\hlstd{(pandginnall}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{)}
\end{alltt}
\begin{verbatim}
##
## FALSE TRUE
## 236 88
\end{verbatim}
\begin{alltt}
\hlstd{chi}\hlkwb{<-}\hlkwd{table}\hlstd{(}\hlkwd{is.na}\hlstd{(pandginnall}\hlopt{$}\hlstd{TOTAL)}\hlopt{==}\hlnum{FALSE}\hlstd{,pandginnall}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{)}
\hlstd{chi}
\end{alltt}
\begin{verbatim}
##
## FALSE TRUE
## FALSE 212 77
## TRUE 24 11
\end{verbatim}
\begin{alltt}
\hlkwd{chisq.test}\hlstd{(chi)}
\end{alltt}
\begin{verbatim}
##
## Pearson's Chi-squared test with Yates' continuity correction
##
## data: chi
## X-squared = 0.15992, df = 1, p-value = 0.6892
\end{verbatim}
\end{kframe}
\end{knitrout}
No enrichment in PanCORONA in our genes under PS.
\end{document}
covid_comp_maic.pdf 0 → 100644
View file @ 77f559a1
File added
covid_comp_maic.tex 0 → 100644
View file @ 77f559a1
\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, maic}
\author{Marie Cariou}
\date{March 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle
\tableofcontents
\newpage
\section{Data}
output from covid\_comp\_dataset.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tablo}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlstr{"primatesVbats.csv"}\hlstd{,}
\hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
Output MAIC formatted by Léa. This table includes the DGINN "score".
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{home}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/"}
\hlstd{workdir}\hlkwb{<-}\hlkwd{paste0}\hlstd{(home,} \hlstr{"CIRI_BIBS_projects/2020_05_Etienne_covid/"}\hlstd{)}
\hlstd{maic}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{"data/covid_comp_maic.txt"}\hlstd{),}
\hlkwc{h}\hlstd{=T)}
\end{alltt}
\end{kframe}
\end{knitrout}
\section{MAIC}
\subsection{Boxplot}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{par}\hlstd{(}\hlkwc{mfrow}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{2}\hlstd{,}\hlnum{1}\hlstd{))}
\hlkwd{boxplot}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nbats,} \hlkwc{notch}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{varwidth}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"score DGINN"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Bats"}\hlstd{)}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning in bxp(list(stats = structure(c(21, 825, 1664, 2860, 5392, 15, 625.5, : some notches went outside hinges ('box'): maybe set notch=FALSE}}\begin{alltt}
\hlkwd{stripchart}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nbats,} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{vertical}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.3}\hlstd{,} \hlkwc{add}\hlstd{=}\hlnum{TRUE}\hlstd{)}
\hlkwd{boxplot}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nprimates,} \hlkwc{notch}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"score DGINN"}\hlstd{,} \hlkwc{ylab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{main}\hlstd{=}\hlstr{"Primates"}\hlstd{)}
\hlkwd{stripchart}\hlstd{(maic}\hlopt{$}\hlstd{rank}\hlopt{~}\hlstd{maic}\hlopt{$}\hlstd{nprimates,} \hlkwc{method}\hlstd{=}\hlstr{"jitter"}\hlstd{,} \hlkwc{vertical}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.3}\hlstd{,} \hlkwc{add}\hlstd{=}\hlnum{TRUE}\hlstd{)}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/boxplot-1}
\end{knitrout}
\subsection{Dotchart}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{maic[maic}\hlopt{$}\hlstd{nbats}\hlopt{>=}\hlnum{3}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"gene"}\hlstd{,} \hlstr{"rank"}\hlstd{,} \hlstr{"nbats"}\hlstd{)]}
\hlstd{tmp}\hlkwb{<-}\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{decreasing} \hlstd{=} \hlnum{TRUE}\hlstd{),]}
\hlstd{tmp}\hlopt{$}\hlstd{col}\hlkwb{<-}\hlstr{"black"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"ACE2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{5}\hlstd{]}\hlkwb{<-}\hlnum{1}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlnum{20}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlnum{3}\hlstd{]}\hlkwb{<-}\hlnum{4}
\hlkwd{dotchart}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{main}\hlstd{=}\hlstr{"Bats DGINN >=3"}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{labels}\hlstd{=tmp}\hlopt{$}\hlstd{gene,} \hlkwc{pch}\hlstd{=tmp}\hlopt{$}\hlstd{pch,} \hlkwc{col}\hlstd{=tmp}\hlopt{$}\hlstd{col)}
\hlkwd{legend}\hlstd{(}\hlstr{"topright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"5 (score DGINN)"}\hlstd{,} \hlstr{"4"}\hlstd{,} \hlstr{"3"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/dotbats-1}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tmp}\hlkwb{<-}\hlstd{maic[maic}\hlopt{$}\hlstd{nprimates}\hlopt{>=}\hlnum{3}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"gene"}\hlstd{,} \hlstr{"rank"}\hlstd{,} \hlstr{"nprimates"}\hlstd{)]}
\hlstd{tmp}\hlkwb{<-}\hlstd{tmp[}\hlkwd{order}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{decreasing} \hlstd{=} \hlnum{TRUE}\hlstd{),]}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{5}\hlstd{]}\hlkwb{<-}\hlnum{1}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlnum{20}
\hlstd{tmp}\hlopt{$}\hlstd{pch[tmp}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlnum{3}\hlstd{]}\hlkwb{<-}\hlnum{4}
\hlstd{tmp}\hlopt{$}\hlstd{col}\hlkwb{<-}\hlstr{"black"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"ACE2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlstd{tmp}\hlopt{$}\hlstd{col[tmp}\hlopt{$}\hlstd{gene}\hlopt{==}\hlstr{"TMPRSS2"}\hlstd{]}\hlkwb{<-}\hlstr{"red"}
\hlkwd{dotchart}\hlstd{(tmp}\hlopt{$}\hlstd{rank,} \hlkwc{main}\hlstd{=}\hlstr{"Primates DGINN >=3"}\hlstd{,} \hlkwc{xlab}\hlstd{=}\hlstr{"rank MAIC"}\hlstd{,} \hlkwc{labels}\hlstd{=tmp}\hlopt{$}\hlstd{gene,} \hlkwc{pch}\hlstd{=tmp}\hlopt{$}\hlstd{pch,} \hlkwc{cex}\hlstd{=}\hlnum{0.8}\hlstd{,} \hlkwc{col}\hlstd{=tmp}\hlopt{$}\hlstd{col)}
\hlkwd{legend}\hlstd{(}\hlstr{"topright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"5 (score DGINN)"}\hlstd{,} \hlstr{"4"}\hlstd{,} \hlstr{"3"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/dotprimates-1}
\end{knitrout}
\section{Pan Corona}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{pancorona}\hlkwb{<-}\hlkwd{read.table}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,} \hlstr{"data/pancorona_S5.csv"}\hlstd{),}
\hlkwc{h}\hlstd{=T,} \hlkwc{fill} \hlstd{=} \hlnum{TRUE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\hlkwd{names}\hlstd{(pancorona)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlkwd{names}\hlstd{(pancorona)[}\hlopt{-}\hlnum{1}\hlstd{])}
\hlcom{# Genes en commun}
\hlstd{pancorona}\hlopt{$}\hlstd{tmp.Gene.name[pancorona}\hlopt{$}\hlstd{tmp.Gene.name} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{tmp.Gene.name]}
\end{alltt}
\begin{verbatim}
## [1] TBK1 MARK3 GIGYF2 MARK2 G3BP1 LARP1 ACE2 PABPC1
## [9] TMPRSS2 AP3B1 CLCC1 CSDE1 HECTD1 MARK1 MEPCE PDE4DIP
## [17] POR PRKAR2B RAB5C RTN4 SRP54 UBAP2 UBAP2L UBXN8
## [25] SPART BZW2 EIF4E2 SMOC1 STOML2 DDX21 FAM98A G3BP2
## [33] MOV10 PABPC4 UPF1
## 105 Levels: ACE2 ANPEP AP3B1 ATXN2L BTF3 BZW2 CKAP5 CLCC1 ... YTHDF2
\end{verbatim}
\begin{alltt}
\hlcom{# Uniquement dans le tableau pancorona}
\hlkwd{sort}\hlstd{(pancorona}\hlopt{$}\hlstd{tmp.Gene.name[(pancorona}\hlopt{$}\hlstd{tmp.Gene.name} \hlopt{%in%} \hlstd{tablo}\hlopt{$}\hlstd{tmp.Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
\end{alltt}
\begin{verbatim}
## [1] ANPEP ATXN2L BTF3 CKAP5 CTSB CTSL
## [7] CYB5R3 DDX1 DDX5 DDX58 DHX9 DNM1L
## [13] EEF1A1 EIF2A EIF3F EIF4B EZR FLNA
## [19] FURIN FUS GSK3A GSK3B HDLBP HNRNPA1
## [25] HNRNPD HNRNPF HNRNPU IFIH1 IGF2BP1 IKBKB
## [31] IKBKE IRF3 ISG15 KPNA3 KPNB1 MYH9
## [37] NCL POLD1 POLR2B PRKRA RBM14 RCHY1
## [43] RPL13A RPL26 RPS13 RPS17 RPS19 RPS9
## [49] SDCBP SERBP1 SGTA SLC1A5 SNAP47 SSB
## [55] STING1 SYNCRIP TANC1 TBCB TMPRSS11D TRAF3
## [61] TUBA4A TUBB2A TUBB4A TUBB6 USP10 VPS36
## [67] XRCC5 XRCC6 YBX1 YTHDF2
## 105 Levels: ACE2 ANPEP AP3B1 ATXN2L BTF3 BZW2 CKAP5 CLCC1 ... YTHDF2
\end{verbatim}
\begin{alltt}
\hlcom{## Uniquement dans tableau }
\hlkwd{sort}\hlstd{(tablo}\hlopt{$}\hlstd{tmp.Gene.name[(tablo}\hlopt{$}\hlstd{tmp.Gene.name} \hlopt{%in%} \hlstd{pancorona}\hlopt{$}\hlstd{tmp.Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
\end{alltt}
\begin{verbatim}
## [1] AAR2 AASS AATF ABCC1 ACAD9 ACADM
## [7] ACSL3 ADAM9 ADAMTS1 AGPS AKAP8 AKAP8L
## [13] AKAP9 ALG11 ALG5 ALG8 ANO6 AP2A2
## [19] AP2M1 ARF6 ATE1 ATP13A3 ATP1B1 ATP6AP1
## [25] ATP6V1A BAG5 BCKDK BRD2 BRD4 CCDC86
## [31] CDK5RAP2 CENPF CEP112 CEP135 CEP250 CEP350
## [37] CEP68 CHMP2A CHPF CHPF2 CISD3 CIT
## [43] CLIP4 CNTRL COL6A1 COLGALT1 COMT COQ8B
## [49] CRTC3 CSNK2A2 CSNK2B CUL2 CWC27 CYB5B
## [55] DCAF7 DCAKD DCTPP1 DDX10 DNAJC11 DNAJC19
## [61] DNMT1 DPH5 DPY19L1 ECSIT EDEM3 EIF4H
## [67] ELOC EMC1 ERC1 ERGIC1 ERLEC1 ERMP1
## [73] ERO1B ERP44 ETFA EXOSC2 EXOSC3 EXOSC5
## [79] EXOSC8 F2RL1 FAM162A FAM8A1 FAR2 FASTKD5
## [85] FBLN5 FBN1 FBN2 FBXL12 FKBP10 FKBP15
## [91] FKBP7 FOXRED2 FYCO1 GCC1 GCC2 GDF15
## [97] GFER GGCX GGH GHITM GLA GNB1
## [103] GNG5 GOLGA2 GOLGA3 GOLGA7 GOLGB1 GORASP1
## [109] GPAA1 GPX1 GRIPAP1 GRPEL1 GTF2F2 HDAC2
## [115] HEATR3 HMOX1 HOOK1 HS2ST1 HS6ST2 HSBP1
## [121] HYOU1 IDE IL17RA IMPDH2 INHBE INTS4
## [127] ITGB1 JAKMIP1 KDELC1 KDELC2 LARP4B LARP7
## [133] LMAN2 LOX MAP7D1 MARC1 MAT2B MDN1
## [139] MIB1 MIPOL1 MOGS MPHOSPH10 MRPS2 MRPS25
## [145] MRPS27 MRPS5 MTCH1 MYCBP2 NARS2 NAT14
## [151] NDFIP2 NDUFAF1 NDUFAF2 NDUFB9 NEK9 NEU1
## [157] NGDN NGLY1 NIN NINL NLRX1 NOL10
## [163] NPC2 NPTX1 NSD2 NUP210 NUP214 NUP54
## [169] NUP58 NUP62 NUP88 NUP98 NUTF2 OS9
## [175] PCNT PCSK5 PCSK6 PDZD11 PIGO PIGS
## [181] PITRM1 PKP2 PLAT PLD3 PLEKHA5 PLEKHF2
## [187] PLOD2 PMPCA PMPCB POFUT1 POLA1 POLA2
## [193] PPIL3 PPT1 PRIM1 PRIM2 PRKACA PRKAR2A
## [199] PRRC2B PSMD8 PTBP2 PTGES2 PUSL1 PVR
## [205] QSOX2 RAB10 RAB14 RAB18 RAB1A RAB2A
## [211] RAB7A RAB8A RAE1 RALA RAP1GDS1 RBM28
## [217] RBM41 RBX1 RDX REEP5 REEP6 RETREG3
## [223] RHOA RIPK1 RNF41 RPL36 RRP9 SAAL1
## [229] SBNO1 SCAP SCARB1 SCCPDH SDF2 SELENOS
## [235] SEPSECS SIL1 SIRT5 SLC25A21 SLC27A2 SLC30A6
## [241] SLC30A7 SLC30A9 SLC44A2 SLC9A3R1 SLU7 SNIP1
## [247] SRP19 SRP72 STC2 STOM SUN2 TAPT1
## [253] TARS2 TBCA TBKBP1 TCF12 THTPA TIMM10
## [259] TIMM10B TIMM29 TIMM8B TIMM9 TLE1 TLE3
## [265] TM2D3 TMED5 TMEM39B TMEM97 TOMM70 TOR1A
## [271] TOR1AIP1 TRIM59 TRMT1 TUBGCP2 TUBGCP3 TYSND1
## [277] UGGT2 USP54 VPS11 VPS39 WASHC4 WFS1
## [283] YIF1A ZC3H18 ZC3H7A ZDHHC5 ZNF318 ZNF503
## [289] ZYG11B
## 324 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ... ZYG11B
\end{verbatim}
\end{kframe}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{pancorona}\hlkwb{<-}\hlstd{pancorona[,}\hlkwd{c}\hlstd{(}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlstr{"TOTAL"}\hlstd{)]}
\hlstd{pandginn}\hlkwb{<-}\hlkwd{na.omit}\hlstd{(}\hlkwd{merge}\hlstd{(pancorona, tablo,} \hlkwc{by}\hlstd{=}\hlstr{"tmp.Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=}\hlnum{TRUE}\hlstd{))}
\hlstd{pandginn}\hlkwb{<-}\hlstd{pandginn[}\hlkwd{order}\hlstd{(pandginn}\hlopt{$}\hlstd{nprimates),]}
\hlstd{pandginn}\hlkwb{<-}\hlstd{pandginn[}\hlkwd{order}\hlstd{(pandginn}\hlopt{$}\hlstd{TOTAL),]}
\hlkwd{dotchart}\hlstd{(}\hlkwd{as.matrix}\hlstd{(pandginn[,}\hlnum{2}\hlstd{]),} \hlkwc{labels} \hlstd{= pandginn}\hlopt{$}\hlstd{tmp.Gene.name,} \hlkwc{xlim}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{5}\hlstd{))}
\hlkwd{points}\hlstd{(pandginn[,}\hlnum{4}\hlstd{],} \hlnum{1}\hlopt{:}\hlkwd{nrow}\hlstd{(pandginn),} \hlkwc{col}\hlstd{=}\hlstr{"blue"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{20}\hlstd{,} \hlkwc{cex}\hlstd{=}\hlnum{0.7}\hlstd{)}
\hlkwd{points}\hlstd{(pandginn[,}\hlnum{3}\hlstd{],} \hlnum{1}\hlopt{:}\hlkwd{nrow}\hlstd{(pandginn),} \hlkwc{col}\hlstd{=}\hlstr{"blue"}\hlstd{,} \hlkwc{pch}\hlstd{=}\hlnum{4}\hlstd{)}
\hlkwd{legend}\hlstd{(}\hlstr{"bottomright"}\hlstd{,} \hlkwd{c}\hlstd{(}\hlstr{"pancorona score"}\hlstd{,} \hlstr{"dginn primate score"}\hlstd{,} \hlstr{"dginn bats score"}\hlstd{),} \hlkwc{pch}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{20}\hlstd{,}\hlnum{4}\hlstd{),} \hlkwc{col}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"black"}\hlstd{,} \hlstr{"blue"}\hlstd{,} \hlstr{"blue"}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/pancorona-1}
\end{knitrout}
\end{document}
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