向系統發育樹添加符號和信息

Question

我正在繪制系統發育樹，我想在已滅絕物種的頂端添加類似“死符號”（例如頭骨）的內容。

我還想在分支時間（例如$ \\ Delta t_i $或數字）上加點標記的帶有乳膠符號的X軸欄。

到目前為止，我只有這棵樹。 在這種情況下，我想在綠色虛線之后添加無效符號。

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

一種可能性是使用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")

帶系統的

#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

我可以看到兩個選項，如何在樹梢上顯示“滅絕”符號。

1. 使用具有適當字體的Unicode符號可以按照此博客進行顯示。
2. 將柵格圖像添加到樹圖上。

以下代碼將在樹的綠色邊緣旁邊顯示一個消光符號 。 它利用此處找到的信息 。

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()