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diff --git a/rnw_scripts/covid_comp_gwas.pdf b/rnw_scripts/covid_comp_gwas.pdf
index 73ed54e9b5727c4f79d5e483dd429487405c0ddf..5949df57007b291f7c627fd31123cd5d090924c8 100644
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diff --git a/rnw_scripts/covid_comp_gwas.tex b/rnw_scripts/covid_comp_gwas.tex
index b2c829c1e346fd612c69b0fdaede15856c331da5..f0300888c2135c0a54c4b10cb416ffcad78bf41b 100644
--- a/rnw_scripts/covid_comp_gwas.tex
+++ b/rnw_scripts/covid_comp_gwas.tex
@@ -309,6 +309,10 @@ GWAS3
\hlstd{gwastab}\hlkwb{<-}\hlstd{gwastab[(gwastab}\hlopt{$}\hlstd{CHR}\hlopt{==}\hlnum{3} \hlopt{&} \hlstd{gwastab}\hlopt{$}\hlstd{POS}\hlopt{>}\hlstd{deb} \hlopt{&} \hlstd{gwastab}\hlopt{$}\hlstd{POS}\hlopt{<}\hlstd{end),]}
\hlstd{gwas1pos}\hlkwb{<-}\hlstd{gwastab}\hlopt{$}\hlstd{POS[gwastab}\hlopt{$}\hlstd{all_inv_var_meta_p}\hlopt{<}\hlstd{thres]}
+
+\hlstd{gwas3tab}\hlkwb{<-}\hlstd{gwastab}
+\hlcom{#gwastab[gwastab$all_inv_var_meta_p<thres & gwastab$POS==45967995,]}
+
\hlstd{file1}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(posref} \hlopt{%in%} \hlstd{gwas1pos,} \hlnum{TRUE}\hlstd{,} \hlnum{FALSE}\hlstd{)}
\hlkwd{sum}\hlstd{(file1)}
\end{alltt}
@@ -353,25 +357,44 @@ Le gene est en antisens co
\hlstd{cds}
\end{alltt}
\begin{verbatim}
-## V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
-## 4 3 CDS 45984856 45984910 ENSG00000163820 ; ENST00000535325 ; exon_number 2 ;
-## 7 3 CDS 45981570 45981676 ENSG00000163820 ; ENST00000535325 ; exon_number 3 ;
-## 9 3 CDS 45979705 45979830 ENSG00000163820 ; ENST00000535325 ; exon_number 4 ;
-## 11 3 CDS 45975239 45975345 ENSG00000163820 ; ENST00000535325 ; exon_number 5 ;
-## 13 3 CDS 45973088 45973231 ENSG00000163820 ; ENST00000535325 ; exon_number 6 ;
-## 15 3 CDS 45969675 45969765 ENSG00000163820 ; ENST00000535325 ; exon_number 7 ;
-## 17 3 CDS 45966277 45968703 ENSG00000163820 ; ENST00000535325 ; exon_number 8 ;
-## 19 3 CDS 45965033 45965125 ENSG00000163820 ; ENST00000535325 ; exon_number 9 ;
-## 21 3 CDS 45964336 45964454 ENSG00000163820 ; ENST00000535325 ; exon_number 10 ;
-## 23 3 CDS 45962225 45962392 ENSG00000163820 ; ENST00000535325 ; exon_number 11 ;
-## 25 3 CDS 45959393 45959542 ENSG00000163820 ; ENST00000535325 ; exon_number 12 ;
-## 27 3 CDS 45958408 45958619 ENSG00000163820 ; ENST00000535325 ; exon_number 13 ;
-## 29 3 CDS 45955249 45955393 ENSG00000163820 ; ENST00000535325 ; exon_number 14 ;
-## 31 3 CDS 45938196 45938255 ENSG00000163820 ; ENST00000535325 ; exon_number 15 ;
-## 33 3 CDS 45936448 45936543 ENSG00000163820 ; ENST00000535325 ; exon_number 16 ;
-## 35 3 CDS 45931071 45931281 ENSG00000163820 ; ENST00000535325 ; exon_number 17 ;
-## 37 3 CDS 45923656 45923765 ENSG00000163820 ; ENST00000535325 ; exon_number 18 ;
-## 39 3 CDS 45921768 45921840 ENSG00000163820 ; ENST00000535325 ; exon_number 19 ;
+## V1 V2 V3 V4 V5 V6 V7 V8
+## 4 3 CDS 45984856 45984910 ENSG00000163820 ; ENST00000535325 ;
+## 7 3 CDS 45981570 45981676 ENSG00000163820 ; ENST00000535325 ;
+## 9 3 CDS 45979705 45979830 ENSG00000163820 ; ENST00000535325 ;
+## 11 3 CDS 45975239 45975345 ENSG00000163820 ; ENST00000535325 ;
+## 13 3 CDS 45973088 45973231 ENSG00000163820 ; ENST00000535325 ;
+## 15 3 CDS 45969675 45969765 ENSG00000163820 ; ENST00000535325 ;
+## 17 3 CDS 45966277 45968703 ENSG00000163820 ; ENST00000535325 ;
+## 19 3 CDS 45965033 45965125 ENSG00000163820 ; ENST00000535325 ;
+## 21 3 CDS 45964336 45964454 ENSG00000163820 ; ENST00000535325 ;
+## 23 3 CDS 45962225 45962392 ENSG00000163820 ; ENST00000535325 ;
+## 25 3 CDS 45959393 45959542 ENSG00000163820 ; ENST00000535325 ;
+## 27 3 CDS 45958408 45958619 ENSG00000163820 ; ENST00000535325 ;
+## 29 3 CDS 45955249 45955393 ENSG00000163820 ; ENST00000535325 ;
+## 31 3 CDS 45938196 45938255 ENSG00000163820 ; ENST00000535325 ;
+## 33 3 CDS 45936448 45936543 ENSG00000163820 ; ENST00000535325 ;
+## 35 3 CDS 45931071 45931281 ENSG00000163820 ; ENST00000535325 ;
+## 37 3 CDS 45923656 45923765 ENSG00000163820 ; ENST00000535325 ;
+## 39 3 CDS 45921768 45921840 ENSG00000163820 ; ENST00000535325 ;
+## V9 V10 V11
+## 4 exon_number 2 ;
+## 7 exon_number 3 ;
+## 9 exon_number 4 ;
+## 11 exon_number 5 ;
+## 13 exon_number 6 ;
+## 15 exon_number 7 ;
+## 17 exon_number 8 ;
+## 19 exon_number 9 ;
+## 21 exon_number 10 ;
+## 23 exon_number 11 ;
+## 25 exon_number 12 ;
+## 27 exon_number 13 ;
+## 29 exon_number 14 ;
+## 31 exon_number 15 ;
+## 33 exon_number 16 ;
+## 35 exon_number 17 ;
+## 37 exon_number 18 ;
+## 39 exon_number 19 ;
\end{verbatim}
\begin{alltt}
\hlstd{cds}\hlopt{$}\hlstd{len}\hlkwb{=}\hlstd{cds}\hlopt{$}\hlstd{V4}\hlopt{-}\hlstd{cds}\hlopt{$}\hlstd{V3}
@@ -663,6 +686,41 @@ Conversion des coordonnées dans example\_fyco1
## 50145 45968043 FALSE TRUE FALSE 1294 FALSE
## 50617 45968515 FALSE FALSE TRUE 819 FALSE
\end{verbatim}
+\begin{alltt}
+\hlstd{gwastab[gwastab}\hlopt{$}\hlstd{all_inv_var_meta_p}\hlopt{<}\hlstd{thres} \hlopt{&} \hlstd{gwastab}\hlopt{$}\hlstd{POS} \hlopt{%in%} \hlkwd{c}\hlstd{(}\hlnum{45966331}\hlstd{,} \hlnum{45966333}\hlstd{,} \hlnum{45966595}\hlstd{,} \hlnum{45967995}\hlstd{,} \hlnum{45968515}\hlstd{),]}
+\end{alltt}
+\begin{verbatim}
+## CHR POS REF ALT SNP all_meta_N
+## 1428785 3 45966331 G T 3:45966331:G:T 23
+## 1428786 3 45966333 T C 3:45966333:T:C 23
+## 1428788 3 45966595 G A 3:45966595:G:A 23
+## 1428791 3 45967995 G A 3:45967995:G:A 23
+## 1428794 3 45968515 T C 3:45968515:T:C 23
+## all_inv_var_meta_beta all_inv_var_meta_sebeta
+## 1428785 0.38699 0.027678
+## 1428786 0.37298 0.027352
+## 1428788 0.38420 0.027682
+## 1428791 0.37943 0.027617
+## 1428794 0.37288 0.027339
+## all_inv_var_meta_p all_inv_var_meta_cases\ttotal
+## 1428785 2.0106e-44 8475
+## 1428786 2.4293e-42 8475
+## 1428788 8.4910e-44 8475
+## 1428791 5.9274e-43 8475
+## 1428794 2.3510e-42 8475
+## all_inv_var_meta_controls all_inv_var_meta_effective
+## 1428785 999425 7110
+## 1428786 999425 7110
+## 1428788 999425 7110
+## 1428791 999425 7110
+## 1428794 999425 7110
+## all_inv_var_het_p all_meta_AF rsid
+## 1428785 0.00081500 0.1221 rs13079478
+## 1428786 0.00107150 0.1230 rs13059238
+## 1428788 0.00155590 0.1222 rs13079869
+## 1428791 0.00039328 0.1224 rs33910087
+## 1428794 0.00111540 0.1230 rs13071283
+\end{verbatim}
\end{kframe}
\end{knitrout}
diff --git a/rnw_scripts/covid_comp_primates_bats.Rnw b/rnw_scripts/covid_comp_primates_bats.Rnw
index c1286403e3fb668166742725010dd6517519fef4..d6aa282e7e46b59fce31ee765177fa18bf112610 100644
--- a/rnw_scripts/covid_comp_primates_bats.Rnw
+++ b/rnw_scripts/covid_comp_primates_bats.Rnw
@@ -54,6 +54,9 @@ library(gplots)
library(Mondrian)
library(UpSetR)
+
+library(ggplot2)
+library(gggenes)
@
@@ -325,6 +328,148 @@ dev.off()
@
+\section{Bat's ACE2}
+
+
+<<>>=
+ACE2<-read.csv(paste0(workdir,
+ "out_tab/covid_comp_alldginn.csv"),
+ h=TRUE, sep=";")
+
+names(ACE2)<-c("row", names(ACE2)[-ncol(ACE2)])
+
+
+ACE2[ACE2$Gene.name=="ACE2",
+ c("bats_Name","bats_MEME_PSS", "bats_BppM1M2_PSS",
+ "bats_BppM7M8_PSS", "bats_codemlM1M2_PSS", "bats_codemlM7M8_PSS")]
+
+PS<-c(24, 27, 91, 214, 218, 444, 583, 692, 705, 709, 723, 725)
+
+
+ACE2_multi<-as.data.frame(cbind(start=1, end=839, molecule="ACE2"))
+
+ACE2_sub<-as.data.frame(cbind(
+ from=c(1, PS), to=c(PS, 839),
+ start=rep(1, length(PS)+1), end=rep(839, length(PS)+1),
+ molecule=rep("ACE2", length(PS)+1),
+ gene=rep("DGINN", length(PS)+1)))
+
+
+
+ACE2_sub$from<-as.numeric(as.character(ACE2_sub$from))
+ACE2_sub$to<-as.numeric(as.character(ACE2_sub$to))
+ACE2_sub$start<-as.numeric(as.character(ACE2_sub$start))
+ACE2_sub$end<-as.numeric(as.character(ACE2_sub$end))
+
+@
+
+<<>>=
+Demo<-c(24, 27, 31, 34, 82, 325)
+
+ACE2_demo<-as.data.frame(cbind(
+ from=Demo, to=Demo,
+ start=rep(1, length(Demo)), end=rep(830, length(Demo)),
+ molecule=rep("ACE2", length(Demo)),
+ gene=rep("Demogines", length(Demo))
+))
+
+ACE2_demo$from<-as.numeric(as.character(ACE2_demo$from))
+ACE2_demo$to<-as.numeric(as.character(ACE2_demo$to))
+ACE2_demo$start<-as.numeric(as.character(ACE2_demo$start))
+ACE2_demo$end<-as.numeric(as.character(ACE2_demo$end))
+@
+Enard,
+https://www.biorxiv.org/content/10.1101/2020.04.20.051656v1.supplementary-material
+
+tab S2, colonne "bats\_tree" seuil 0.05
+<<>>=
+Frank<-c(24, 27, 31, 35, 42, 321, 322, 326, 354)
+
+ACE2_Frank<-as.data.frame(cbind(
+ from=Frank, to=Frank,
+ start=rep(1, length(Frank)), end=rep(839, length(Frank)),
+ molecule=rep("ACE2", length(Frank)),
+ gene=rep("Frank", length(Frank))
+))
+
+ACE2_Frank$from<-as.numeric(as.character(ACE2_Frank$from))
+ACE2_Frank$to<-as.numeric(as.character(ACE2_Frank$to))
+ACE2_Frank$start<-as.numeric(as.character(ACE2_Frank$start))
+ACE2_Frank$end<-as.numeric(as.character(ACE2_Frank$end))
+
+
+ACE2_Frank
+@
+
+
+
+<<1_ACE2_comp, fig.path="../figure/">>=
+
+
+g<- ggplot(ACE2_multi,
+ aes(xmin = start, xmax = end, y = molecule, fill = "white"))
+g <- g + geom_gene_arrow(arrowhead_height = unit(0, "mm"),
+ arrowhead_width = unit(0, "mm"), fill="white", color="black")
+g <- g + geom_subgene_arrow(data = ACE2_sub,
+ arrowhead_height = unit(0, "mm"), arrowhead_width = unit(0, "mm"),
+ arrow_body_height = unit(10, "mm"),
+ aes(xmin = start, xmax = end, y = molecule, fill = "white",
+ xsubmin = from, xsubmax = to), color="black", alpha=1, fill="white")
+g <- g + geom_subgene_arrow(data = ACE2_demo,
+ arrowhead_height = unit(0, "mm"), arrowhead_width = unit(0, "mm"),
+ arrow_body_height = unit(10, "mm"),
+ aes(xmin = start, xmax = end, y = molecule, fill = "white",
+ xsubmin = from, xsubmax = to), color="blue", alpha=1)
+g <- g + geom_subgene_arrow(data = ACE2_Frank,
+ arrowhead_height = unit(0, "mm"), arrowhead_width = unit(0, "mm"),
+ arrow_body_height = unit(10, "mm"),
+ aes(xmin = start, xmax = end, y = molecule, fill = "white",
+ xsubmin = from, xsubmax = to), color="green", alpha=1, fill="white")
+g <- g + theme_genes()
+
+g
+@
+
+
+<<1_ACE2_comp2, fig.path="../figure/", fig.height=2>>=
+
+ACE2_multi
+ACE2_sub
+
+
+g<- ggplot(ACE2_sub,
+ aes(xmin = start, xmax = end, y = gene, fill = "white"))
+g <- g + geom_gene_arrow(arrowhead_height = unit(0, "mm"),
+ arrowhead_width = unit(0, "mm"), fill="white", color="black")
+g <- g + geom_subgene_arrow(data = ACE2_sub,
+ arrowhead_height = unit(0, "mm"), arrowhead_width = unit(0, "mm"),
+ arrow_body_height = unit(14, "mm"),
+ aes(xmin = start, xmax = end, y = gene, fill = "white",
+ xsubmin = from, xsubmax = to), color="black", alpha=1, fill="white")
+g <- g + geom_subgene_arrow(data = ACE2_demo,
+ arrowhead_height = unit(0, "mm"), arrowhead_width = unit(0, "mm"),
+ arrow_body_height = unit(12, "mm"),
+ aes(xmin = start, xmax = end, y = gene, fill = "white",
+ xsubmin = from, xsubmax = to), color="blue", alpha=1)
+g <- g + geom_subgene_arrow(data = ACE2_Frank,
+ arrowhead_height = unit(0, "mm"), arrowhead_width = unit(0, "mm"),
+ arrow_body_height = unit(12, "mm"),
+ aes(xmin = start, xmax = end, y = gene, fill = "white",
+ xsubmin = from, xsubmax = to), color="green", alpha=1, fill="white")
+#g <- g + theme_genes()
+
+g
+
+
+
+
+
+
+
+
+@
\end{document}
+
+
diff --git a/rnw_scripts/covid_comp_primates_bats.pdf b/rnw_scripts/covid_comp_primates_bats.pdf
index 9177e719b2af39c45c5711fbc115251677503bc7..d7393f5c27e7113d748a3b3e323631cb48f8de51 100644
Binary files a/rnw_scripts/covid_comp_primates_bats.pdf and b/rnw_scripts/covid_comp_primates_bats.pdf differ
diff --git a/rnw_scripts/covid_comp_primates_bats.tex b/rnw_scripts/covid_comp_primates_bats.tex
index 04feffeacc5517f03de60dece92f2483d840e01d..54f17e5577af1e8015e7467fc27735ae56c28d9e 100644
--- a/rnw_scripts/covid_comp_primates_bats.tex
+++ b/rnw_scripts/covid_comp_primates_bats.tex
@@ -119,6 +119,9 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwd{library}\hlstd{(Mondrian)}
\hlkwd{library}\hlstd{(UpSetR)}
+
+\hlkwd{library}\hlstd{(ggplot2)}
+\hlkwd{library}\hlstd{(gggenes)}
\end{alltt}
\end{kframe}
\end{knitrout}
@@ -145,7 +148,8 @@ I will merge the 2 tables.
\hlkwd{names}\hlstd{(dginnY)}
\end{alltt}
\begin{verbatim}
-## [1] "Gene" "Omega" "Method" "PosSel" "PValue" "NbSites" "PSS"
+## [1] "Gene" "Omega" "Method" "PosSel" "PValue" "NbSites"
+## [7] "PSS"
\end{verbatim}
\end{kframe}
\end{knitrout}
@@ -527,6 +531,207 @@ Variations of these figures (genes ordered according to the proportion of PS sit
\end{kframe}
\end{knitrout}
+\section{Bat's ACE2}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{ACE2}\hlkwb{<-}\hlkwd{read.csv}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
+ \hlstr{"out_tab/covid_comp_alldginn.csv"}\hlstd{),}
+ \hlkwc{h}\hlstd{=}\hlnum{TRUE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{";"}\hlstd{)}
+
+\hlkwd{names}\hlstd{(ACE2)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"row"}\hlstd{,} \hlkwd{names}\hlstd{(ACE2)[}\hlopt{-}\hlkwd{ncol}\hlstd{(ACE2)])}
+
+
+\hlstd{ACE2[ACE2}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"ACE2"}\hlstd{,}
+ \hlkwd{c}\hlstd{(}\hlstr{"bats_Name"}\hlstd{,}\hlstr{"bats_MEME_PSS"}\hlstd{,} \hlstr{"bats_BppM1M2_PSS"}\hlstd{,}
+ \hlstr{"bats_BppM7M8_PSS"}\hlstd{,} \hlstr{"bats_codemlM1M2_PSS"}\hlstd{,} \hlstr{"bats_codemlM7M8_PSS"}\hlstd{)]}
+\end{alltt}
+\begin{verbatim}
+## bats_Name
+## 7 ACE2
+## bats_MEME_PSS
+## 7 3, 7, 24, 27, 39, 67, 74, 92, 93, 107, 120, 145, 187, 218, 233, 301, 313, 316, 331, 336, 444, 546, 583, 601, 624, 630, 632, 684, 692, 709, 723, 731, 793
+## bats_BppM1M2_PSS
+## 7 24, 91, 214, 218, 444, 583, 692, 705, 709, 723, 725
+## bats_BppM7M8_PSS
+## 7 24, 27, 91, 214, 218, 444, 583, 692, 705, 709, 723, 725
+## bats_codemlM1M2_PSS
+## 7 24, 91, 214, 218, 444, 583, 692, 705, 709, 723, 725
+## bats_codemlM7M8_PSS
+## 7 24, 27, 91, 155, 214, 218, 233, 444, 546, 583, 692, 705, 709, 723, 725
+\end{verbatim}
+\begin{alltt}
+\hlstd{PS}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlnum{24}\hlstd{,} \hlnum{27}\hlstd{,} \hlnum{91}\hlstd{,} \hlnum{214}\hlstd{,} \hlnum{218}\hlstd{,} \hlnum{444}\hlstd{,} \hlnum{583}\hlstd{,} \hlnum{692}\hlstd{,} \hlnum{705}\hlstd{,} \hlnum{709}\hlstd{,} \hlnum{723}\hlstd{,} \hlnum{725}\hlstd{)}
+
+
+\hlstd{ACE2_multi}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(}\hlkwd{cbind}\hlstd{(}\hlkwc{start}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{end}\hlstd{=}\hlnum{839}\hlstd{,} \hlkwc{molecule}\hlstd{=}\hlstr{"ACE2"}\hlstd{))}
+
+\hlstd{ACE2_sub}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(}\hlkwd{cbind}\hlstd{(}
+ \hlkwc{from}\hlstd{=}\hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{, PS),} \hlkwc{to}\hlstd{=}\hlkwd{c}\hlstd{(PS,} \hlnum{839}\hlstd{),}
+ \hlkwc{start}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlnum{1}\hlstd{,} \hlkwd{length}\hlstd{(PS)}\hlopt{+}\hlnum{1}\hlstd{),} \hlkwc{end}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlnum{839}\hlstd{,} \hlkwd{length}\hlstd{(PS)}\hlopt{+}\hlnum{1}\hlstd{),}
+ \hlkwc{molecule}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlstr{"ACE2"}\hlstd{,} \hlkwd{length}\hlstd{(PS)}\hlopt{+}\hlnum{1}\hlstd{),}
+ \hlkwc{gene}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlstr{"DGINN"}\hlstd{,} \hlkwd{length}\hlstd{(PS)}\hlopt{+}\hlnum{1}\hlstd{)))}
+
+
+
+\hlstd{ACE2_sub}\hlopt{$}\hlstd{from}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_sub}\hlopt{$}\hlstd{from))}
+\hlstd{ACE2_sub}\hlopt{$}\hlstd{to}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_sub}\hlopt{$}\hlstd{to))}
+\hlstd{ACE2_sub}\hlopt{$}\hlstd{start}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_sub}\hlopt{$}\hlstd{start))}
+\hlstd{ACE2_sub}\hlopt{$}\hlstd{end}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_sub}\hlopt{$}\hlstd{end))}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{Demo}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlnum{24}\hlstd{,} \hlnum{27}\hlstd{,} \hlnum{31}\hlstd{,} \hlnum{34}\hlstd{,} \hlnum{82}\hlstd{,} \hlnum{325}\hlstd{)}
+
+\hlstd{ACE2_demo}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(}\hlkwd{cbind}\hlstd{(}
+ \hlkwc{from}\hlstd{=Demo,} \hlkwc{to}\hlstd{=Demo,}
+ \hlkwc{start}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlnum{1}\hlstd{,} \hlkwd{length}\hlstd{(Demo)),} \hlkwc{end}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlnum{830}\hlstd{,} \hlkwd{length}\hlstd{(Demo)),}
+ \hlkwc{molecule}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlstr{"ACE2"}\hlstd{,} \hlkwd{length}\hlstd{(Demo)),}
+ \hlkwc{gene}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlstr{"Demogines"}\hlstd{,} \hlkwd{length}\hlstd{(Demo))}
+\hlstd{))}
+
+\hlstd{ACE2_demo}\hlopt{$}\hlstd{from}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_demo}\hlopt{$}\hlstd{from))}
+\hlstd{ACE2_demo}\hlopt{$}\hlstd{to}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_demo}\hlopt{$}\hlstd{to))}
+\hlstd{ACE2_demo}\hlopt{$}\hlstd{start}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_demo}\hlopt{$}\hlstd{start))}
+\hlstd{ACE2_demo}\hlopt{$}\hlstd{end}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_demo}\hlopt{$}\hlstd{end))}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+Enard,
+https://www.biorxiv.org/content/10.1101/2020.04.20.051656v1.supplementary-material
+
+tab S2, colonne "bats\_tree" seuil 0.05
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{Frank}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlnum{24}\hlstd{,} \hlnum{27}\hlstd{,} \hlnum{31}\hlstd{,} \hlnum{35}\hlstd{,} \hlnum{42}\hlstd{,} \hlnum{321}\hlstd{,} \hlnum{322}\hlstd{,} \hlnum{326}\hlstd{,} \hlnum{354}\hlstd{)}
+
+\hlstd{ACE2_Frank}\hlkwb{<-}\hlkwd{as.data.frame}\hlstd{(}\hlkwd{cbind}\hlstd{(}
+ \hlkwc{from}\hlstd{=Frank,} \hlkwc{to}\hlstd{=Frank,}
+ \hlkwc{start}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlnum{1}\hlstd{,} \hlkwd{length}\hlstd{(Frank)),} \hlkwc{end}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlnum{839}\hlstd{,} \hlkwd{length}\hlstd{(Frank)),}
+ \hlkwc{molecule}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlstr{"ACE2"}\hlstd{,} \hlkwd{length}\hlstd{(Frank)),}
+ \hlkwc{gene}\hlstd{=}\hlkwd{rep}\hlstd{(}\hlstr{"Frank"}\hlstd{,} \hlkwd{length}\hlstd{(Frank))}
+\hlstd{))}
+
+\hlstd{ACE2_Frank}\hlopt{$}\hlstd{from}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_Frank}\hlopt{$}\hlstd{from))}
+\hlstd{ACE2_Frank}\hlopt{$}\hlstd{to}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_Frank}\hlopt{$}\hlstd{to))}
+\hlstd{ACE2_Frank}\hlopt{$}\hlstd{start}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_Frank}\hlopt{$}\hlstd{start))}
+\hlstd{ACE2_Frank}\hlopt{$}\hlstd{end}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ACE2_Frank}\hlopt{$}\hlstd{end))}
+
+
+\hlstd{ACE2_Frank}
+\end{alltt}
+\begin{verbatim}
+## from to start end molecule gene
+## 1 24 24 1 839 ACE2 Frank
+## 2 27 27 1 839 ACE2 Frank
+## 3 31 31 1 839 ACE2 Frank
+## 4 35 35 1 839 ACE2 Frank
+## 5 42 42 1 839 ACE2 Frank
+## 6 321 321 1 839 ACE2 Frank
+## 7 322 322 1 839 ACE2 Frank
+## 8 326 326 1 839 ACE2 Frank
+## 9 354 354 1 839 ACE2 Frank
+\end{verbatim}
+\end{kframe}
+\end{knitrout}
+
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{g}\hlkwb{<-} \hlkwd{ggplot}\hlstd{(ACE2_multi,}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= molecule,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{))}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_gene_arrow}\hlstd{(}\hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{fill}\hlstd{=}\hlstr{"white"}\hlstd{,} \hlkwc{color}\hlstd{=}\hlstr{"black"}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_subgene_arrow}\hlstd{(}\hlkwc{data} \hlstd{= ACE2_sub,}
+ \hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrow_body_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{10}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= molecule,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{,}
+ \hlkwc{xsubmin} \hlstd{= from,} \hlkwc{xsubmax} \hlstd{= to),} \hlkwc{color}\hlstd{=}\hlstr{"black"}\hlstd{,} \hlkwc{alpha}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{fill}\hlstd{=}\hlstr{"white"}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_subgene_arrow}\hlstd{(}\hlkwc{data} \hlstd{= ACE2_demo,}
+ \hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrow_body_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{10}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= molecule,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{,}
+ \hlkwc{xsubmin} \hlstd{= from,} \hlkwc{xsubmax} \hlstd{= to),} \hlkwc{color}\hlstd{=}\hlstr{"blue"}\hlstd{,} \hlkwc{alpha}\hlstd{=}\hlnum{1}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_subgene_arrow}\hlstd{(}\hlkwc{data} \hlstd{= ACE2_Frank,}
+ \hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrow_body_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{10}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= molecule,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{,}
+ \hlkwc{xsubmin} \hlstd{= from,} \hlkwc{xsubmax} \hlstd{= to),} \hlkwc{color}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{alpha}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{fill}\hlstd{=}\hlstr{"white"}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{theme_genes}\hlstd{()}
+
+\hlstd{g}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{../figure/1_ACE2_comp-1}
+\end{knitrout}
+
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{ACE2_multi}
+\end{alltt}
+\begin{verbatim}
+## start end molecule
+## 1 1 839 ACE2
+\end{verbatim}
+\begin{alltt}
+\hlstd{ACE2_sub}
+\end{alltt}
+\begin{verbatim}
+## from to start end molecule gene
+## 1 1 24 1 839 ACE2 DGINN
+## 2 24 27 1 839 ACE2 DGINN
+## 3 27 91 1 839 ACE2 DGINN
+## 4 91 214 1 839 ACE2 DGINN
+## 5 214 218 1 839 ACE2 DGINN
+## 6 218 444 1 839 ACE2 DGINN
+## 7 444 583 1 839 ACE2 DGINN
+## 8 583 692 1 839 ACE2 DGINN
+## 9 692 705 1 839 ACE2 DGINN
+## 10 705 709 1 839 ACE2 DGINN
+## 11 709 723 1 839 ACE2 DGINN
+## 12 723 725 1 839 ACE2 DGINN
+## 13 725 839 1 839 ACE2 DGINN
+\end{verbatim}
+\begin{alltt}
+\hlstd{g}\hlkwb{<-} \hlkwd{ggplot}\hlstd{(ACE2_sub,}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= gene,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{))}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_gene_arrow}\hlstd{(}\hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{fill}\hlstd{=}\hlstr{"white"}\hlstd{,} \hlkwc{color}\hlstd{=}\hlstr{"black"}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_subgene_arrow}\hlstd{(}\hlkwc{data} \hlstd{= ACE2_sub,}
+ \hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrow_body_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{14}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= gene,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{,}
+ \hlkwc{xsubmin} \hlstd{= from,} \hlkwc{xsubmax} \hlstd{= to),} \hlkwc{color}\hlstd{=}\hlstr{"black"}\hlstd{,} \hlkwc{alpha}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{fill}\hlstd{=}\hlstr{"white"}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_subgene_arrow}\hlstd{(}\hlkwc{data} \hlstd{= ACE2_demo,}
+ \hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrow_body_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{12}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= gene,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{,}
+ \hlkwc{xsubmin} \hlstd{= from,} \hlkwc{xsubmax} \hlstd{= to),} \hlkwc{color}\hlstd{=}\hlstr{"blue"}\hlstd{,} \hlkwc{alpha}\hlstd{=}\hlnum{1}\hlstd{)}
+\hlstd{g} \hlkwb{<-} \hlstd{g} \hlopt{+} \hlkwd{geom_subgene_arrow}\hlstd{(}\hlkwc{data} \hlstd{= ACE2_Frank,}
+ \hlkwc{arrowhead_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),} \hlkwc{arrowhead_width} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{0}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwc{arrow_body_height} \hlstd{=} \hlkwd{unit}\hlstd{(}\hlnum{12}\hlstd{,} \hlstr{"mm"}\hlstd{),}
+ \hlkwd{aes}\hlstd{(}\hlkwc{xmin} \hlstd{= start,} \hlkwc{xmax} \hlstd{= end,} \hlkwc{y} \hlstd{= gene,} \hlkwc{fill} \hlstd{=} \hlstr{"white"}\hlstd{,}
+ \hlkwc{xsubmin} \hlstd{= from,} \hlkwc{xsubmax} \hlstd{= to),} \hlkwc{color}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{alpha}\hlstd{=}\hlnum{1}\hlstd{,} \hlkwc{fill}\hlstd{=}\hlstr{"white"}\hlstd{)}
+\hlcom{#g <- g + theme_genes()}
+
+\hlstd{g}
+\end{alltt}
+\end{kframe}
+\includegraphics[width=\maxwidth]{../figure/1_ACE2_comp2-1}
+\end{knitrout}
\end{document}
+
+