向系统发育树添加符号和信息

Question

我正在绘制一个系统发育树，我想在灭绝物种的尖端添加类似“死亡符号”（例如头骨）的东西。

我还想在分支时间（例如$ \ Delta t_i $或数字）中添加带有乳胶符号的x轴条，用点标记。

到目前为止我所拥有的是这棵树。在这种情况下，我想在绿色虚线后面添加死符号。

library(ape)
rec1 = '((B:1,A:1):1,(F:1,C:1.5):0.5);'
rec1 = read.tree(text = rec1)
plot(rec1,show.tip.label = F,edge.color = c("black","black","black","black","darkgreen","black"),edge.width = 2,edge.lty = c(rep(1,4),4,1))

Answer 1

一种可能性是使用ggtree。如： https://guangchuangyu.github.io/2018/03/annotating-phylogenetic-tree-with-images-using-ggtree-and-ggimage/

#source("https://bioconductor.org/biocLite.R")
#biocLite("BiocUpgrade") # you may need this
#biocLite("ggtree")
library(ggtree)

tree<-rtree(10)
pg<-ggtree(tree)
d <- data.frame(node = as.character(10:15),
                images = c("https://i.imgur.com/8VA9cYw.png",
                           "https://i.imgur.com/XYM1T2x.png",
                           "https://i.imgur.com/EQs5ZZe.png",
                           "https://i.imgur.com/2xin0UK.png",
                           "https://i.imgur.com/hbftayl.png",
                           "https://i.imgur.com/3wDHW8n.png"))
pg %<+% d + geom_nodelab(aes(image=images), geom="image")

有phylopic

#install.packages('rphylopic')
library(rphylopic)
string<-name_search(text = "Homo sapiens")
selectstr<-string[2,]
string2<-name_images(uuid = selectstr)$same[[1]]$uid
tree<-rtree(10)
phylopic_info <- data.frame(node = c(12,13),
                            phylopic = string2)
nt<-ggtree(tree) 
nt %<+% phylopic_info + 
  geom_nodelab(aes(image=phylopic), geom="phylopic", alpha=.5, color='steelblue')

Answer 2

我可以看到两个选项如何在树尖上显示“灭绝”符号。

1. 使用具有适当字体的Unicode符号，该字符可以按this blog显示。
2. 将光栅图像添加到树形图上。

以下代码将在树的绿色边缘旁边显示extinction symbol。它利用了here找到的信息。

library(jpeg)
logo <- readJPEG("Downloads/Symbol1.jpg")
logo2 <- as.raster(logo)
r <- nrow(logo2)/ncol(logo2) # aspect ratio
s <- 0.4 # symbol size

# display plot to obtain its size
plot(rec1, edge.color = c("black","black","black","black","darkgreen","black"),
    edge.width = 2, edge.lty = c(rep(1,4),4,1))
lims <- par("usr") # plot area size
file_r <- (lims[2]-lims[1]) / (lims[4]-lims[3]) # aspect ratio for the file
file_s <- 480   # file size

# save tree with added symbol
png("tree_logo.png", height=file_s, width=file_s*file_r)
plot(rec1, show.tip.label = F, 
    edge.color = c("black","black","black","black","darkgreen","black"), 
    edge.width = 2, edge.lty = c(rep(1,4),4,1))
rasterImage(logo2, 1.6, 2.8, 1.6+s/r, 2.8+s)

# add axis
axisPhylo()
mtext(expression(Delta*italic("t")["i"]), side = 1, line = 3)
dev.off()