In phylotastic/rphylotastic: An R Interface to 'Phylotastic' Web Services

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "# >"
)

This is an example to use rphylotastic tools to contextualize phylogenetic relationships. The main packages are not yet installable via CRAN, so to install them you have to use the install_github function from the package devtools:

install.packages("devtools") # this installs devtools package
library(devtools) # this loads the package contents into the workspace
# the following two lines install datelife and rphylotastic from development repositories
install_github("phylotastic/datelife") 
install_github("phylotastic/rphylotastic")

library(datelife)
library(rphylotastic)

Now, say you are hiking in Yellowstone with ypur students, and yu want them to get the phylogenetic relationships of the organisms they spotted during the hike. The function taxa_common_to_sicentific will get the scientific names from common names you provide. In this example, the student is interested in birds:

birds_I_saw = taxa_common_to_scientific(c("Osprey", "House sparrow", 
    "Mallard duck", "American Robin", "song sparrow", "mourning dove", 
    "house wren"))

This gets the species that will provide phylogenetic context to the focal species:

yellowstone_birds <- url_get_scientific_names(URL=
    "https://www.nps.gov/yell/learn/nature/upload/BirdChecklist2014.pdf")

Then, we will get the tree with dates containing both the focal species and their phylogenetic context

yellowstone_bird_tree <- datelife::datelife_search(
    taxa_get_otol_tree(yellowstone_birds), summary_format 
    = "phylo_median")

To plot the tree you will need some ape package functions:

library(ape)

par(xpd = NA)
ape::plot.phylo(yellowstone_bird_tree,
      tip.color = ifelse(yellowstone_bird_tree$tip.label%in%birds_I_saw, "red", "black"),
      cex=0.3, type = "fan", edge.width = 0.45, label.offset = 1.5)

We can add taxonomic labels such as family names. If you have a table with the corresponding families to each species on the tip of the tree, you can type it in as a vector, or read it with read.table function. If you do not have that info, you can pull it using a datelife function called get_ott_clade.

yellowstone_bird_fams = get_ott_clade(ott_ids = yellowstone_bird_tree$ott_ids,
        ott_rank = "family")

Then, we will make a list of species within families, and feed it to the function that will plot the arcs: We will call this list tipsies

families = unique(names(yellowstone_bird_fams$family))
tipsies = sapply(families, function(x) 
    yellowstone_bird_tree$tip.label[names(yellowstone_bird_fams$family)%in%x])

Now we are gonna set the colors of the arc lines in the variable arc_grays and their position in arc_line_offset:

seede = set.seed(100)
arc_grays = sample(gray.colors(n = length(tipsies)), length(tipsies))
arc_line_offset = rep(1.63, length(tipsies))

Finally, we need to costumize the position of family name labels so they do not overlap. For that we made two functions. The first one simply changes the horizontal position, modifying arc_line_offset and allowing labels to be closer or further away from the arcs. And then we ended up tweaking the position for certain families that were still overlapping too much.

get_arc_label_offset <- function(alineo){
    res <- alineo + 0.05
    res[29] <- res[29]-0.0 #laridae
    res[30] <- res[30]+0.05
    res[31] <- res[31]-0.18 #recurvirostridae
    res[34] <- res[34]-0.16 #ardeidae
    res[37] <- res[37]-0.19 #gaviidae
    return(res)
}
arc_label_offset = get_arc_label_offset(arc_line_offset)

The second function changes their actual position in degressa round the plot. index indicates the family that we want to change, and degree sets the new degree that we want to set for the label:

make_label_degree <- function(length, index, degree){
  deg <- rep(NA, length)
  for(i in seq(length(index))){
    deg[index[i]] <- degree[i]
  }
  return(deg)
}
our_label_degree = make_label_degree(length(families),
  index = c(5,6,7,14,15, 17, 31, 32, 34, 36, 37, 38, 39, 40, 43, 44),
  degree = c(24, 26, 28, 112.5, 116.5, 125, 270, 275, 278, 293, 285, 297, 301, 304, 314, 316))

Finally we plot the tree again and add the labels with the rphylotasic function arclabels:

par(xpd = TRUE, mai = rep(1,4))
ape::plot.phylo(yellowstone_bird_tree,
      tip.color = ifelse(yellowstone_bird_tree$tip.label%in%birds_I_saw, "red", "black"),
      cex=0.3, type = "fan", edge.width = 0.45, label.offset = 1.5)
      for(i in seq(length(tipsies))){
        # cat(i, families[i], "\n")
        arclabels(phy = yellowstone_bird_tree, text = families[i], tips = tipsies[[i]],
            orientation = "horizontal", col = arc_grays[i], lwd = 4,
            lab.offset = arc_label_offset[i], ln.offset = arc_line_offset[i],
            cex = 0.5, label_degree = our_label_degree[i])
      }