--- title: "Vision loss evo" output: html_document --- knitr::opts_chunk$set( echo = FALSE, fig.path = './Analysis/plot-', cache = TRUE ) ##Load up packages, data and tree ```{r } setwd("./Data/") require(phytools) require(ggtree) require(dispRity) require(RRphylo) tree <-read.tree ("tree.nwk") data <-read.csv ("acuityblind.csv",row.names=1) clean.data(data,tree) dat <- as.data.frame(data$VA) row.names(dat)<-row.names(data) dat$weight <- log(data$X5.1_AdultBodyMass_g) names(dat) <- c("VA", "W") dat$relVA <- c(dat$VA/dat$W) names(dat) <- data$Bin names(dat) <- c("VA", "W", "relVA") ``` ##ANC ```{r , include=FALSE} tree$edge.length[which(tree$edge.length == 0)] <- 0.01*median(tree$edge.length[-which(tree$edge.length == 0)]) tree <- force.ultrametric(tree,method="extend") anc <- fastAnc(tree,data$VA, vars=TRUE,CI=TRUE, REML = 1) #anc1<-fastAnc(tree,dat$relVA,vars=TRUE,CI=TRUE, REML = 1, na.omit = TRUE) plot(tree,no.margin=TRUE,edge.width=2,cex=0.7) nodelabels(text=anc$VA,frame="none",adj=c(1.1,-0.4), cex=0.5) ``` ##Plotting ```{r, include=TRUE} #pdf(file="treeblind.pdf",width=10,height=10) fancyTree(tree,type="scattergram",X=as.matrix(dat),A=as.matrix(anc),control=list(spin=FALSE),label="horizontal") #dev.off() #OR dat1 <- data$VA names(dat1) <- row.names(dat) #pdf(file="treeblind1.pdf",width=10,height=10) obj1<-contMap(tree,dat1,fsize=c(0.6,1),outline=FALSE) #plot(obj1,direction="leftwards") #dev.off() plot(obj1,type="fan",legend=0.7*max(nodeHeights(tree)), fsize=c(0.7,0.9)) phenogram(tree,dat1,fsize=0.6,spread.labels=TRUE,spread.cost=c(1,0)) fancyTree(tree,type="phenogram95",x=dat1,spread.cost=c(1,0)) #not working obj<-contMap(tree,exp(dat1),plot=FALSE) plotTree.wBars(obj$tree,dat1,method="plotSimmap", tip.labels=TRUE,fsize=0.7,colors=obj$cols,type="fan",scale=0.002) add.color.bar(1.0,obj$cols,title="trait value",lims=obj$lims,prompt=FALSE, x=0.9*par()$usr[1],y=0.9*par()$usr[3]) ``` ##Plotting 2 ```{r, include=TRUE} #resetting the plot space #old.par <- par(mar = c(0, 0, 0, 0)) #par(old.par) pdf(file="treeblind2.pdf",width=10,height=10) plot(tree,label.offset=5, cex= 0.7) nodelabels(cex=anc$ace/30,pch=16) tiplabels(cex=dat$VA/70,pch=16) dev.off() ``` RRphylo ```{r} RR <- RRphylo(tree, dat1) #search.conv(RR,tree,dat1, PGLSf=TRUE,nsim=1000,rsim=1000, clus=.5, min.dist = 3, foldername ="Data") search.shift(RR, auto.recognize = "yes", test.single = "yes", status.type= "clade", nrep = 10000, f=2, foldername ="Data") #cov = can add covariate #### Circular tree plot np <- ggtree(tree, layout="circular") + geom_hilight(node=176, fill="firebrick2", alpha=.6) + geom_hilight(node=224, fill="limegreen", alpha=.6) + geom_hilight(node=198, fill="firebrick2", alpha=.6) np + geom_cladelabel(176, 'Chiroptera', angle=315, hjust = "center", offset.text=13, barsize=3.5, color='red4', offset = 2.5, fontsize = 5) + geom_cladelabel(224, 'Haplorhini', angle=70, hjust = "center", offset.text=13, barsize=3.5, color = 'darkgreen', offset = 2.5, fontsize = 5) + geom_cladelabel(198, 'Rodentia', angle=355, hjust = "center", offset.text=13, barsize=3.5, color='red4', offset = 2.5, fontsize = 5) + geom_cladelabel(238, 'Afrotheria', angle=315, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(123, 'Marsupialia', angle=295, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(158, 'Artiodactyla', angle=60, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(143, 'Carnivora', angle=10, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(157, 'Perissodactyla', angle=345, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(138, 'Eulipotyphla', angle=280, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(219, 'Strepsirrhini', angle=40, hjust = "center", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 3) + geom_cladelabel(237, 'Scandentia', angle=26, hjust = "left", offset.text=13, barsize=1, color='black', offset = 2.5, fontsize = 2.5) ```