put all tanglegram in dataset script and change colors

covid_comp_dataset.Rnw

@@ -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
@@ -329,7 +329,6 @@ tmp<-as.data.frame(tmp)
 matbats<-hclust(dist(tmp$nbats))
 matpri<-hclust(dist(tmp$nprimates))
 
-
 tmp[order(tmp$nbats),]
 
 dendpri<-as.dendrogram(matpri)
@@ -346,14 +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,
@@ -366,12 +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}