Quick & easy phylogenetic visualizations and trait analysis in r

Author: Russell Gray

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Required Data

obtained from: ​http://snakedatabase.org/pages/ld50.php

tblld50.csv
File Size:	10 kb
File Type:	csv

Download File

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Required packages 
remotes::install_github("GuangchuangYu/treeio")
install.packages("BiocManager")
BiocManager::install("ggtree")

You will need to use the Install.Packages() function before you open these in the library
library("ape")
library("taxize")
library("rentrez")
library("phytools")
library("select")
library("treeio")
library("ggtree")
library("data.tree")
library("tidytree")
library("ggplot2")
library("dplyr")


This book is super helpful I encourage everyone to check it out!
https://yulab-smu.github.io/treedata-book/chapter2.html

#############################################################
#Set your workdesk
setwd("C:/Users/Russell/Desktop/venom")

This is the attached data file from above
#read in your data with species names and traits you would like to use
dat<-read.csv("TBLld50.csv")

#pull the species names column out to create a species list string
sp_list<-as.character(dat$Scientific.Name)

#set your ncbi key. If you don't have one, you can get it 
#by registering an account with ncbi 
set_entrez_key("xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx")
Sys.getenv("ENTREZ_KEY")


#obtain cladistic data on your species list from ncbi
taxise_sp <- classification(sp_list, db = "ncbi")

#Coerce your species list into a classtree object
tax_tree <- class2tree(taxise_sp)

#Pull the phylo object from the classtree for plotting
tax_phylo <- tax_tree$phylo

#plot your basic tree to see what it looks like change x/y values according 
#to your own data
new.snake.tree %>% 
  ggtree() + 
  geom_tiplab(size=1) +
  theme_tree2() + 
  xlim(0, 90)

#Now that the tree works lets write it into a newick file in case
#we need it later
write.tree(tax_phylo, file = "Snake_Tree")

#import the tree file again just to make sure the function works
#give it an appropriate name for your species (note: this function works with several different tree files, so if you have the ability to import a n existing tree with proper branch distance metrics, that would be ideal)
snake.tree <- read.newick(file = "Snake_Tree")


#now lets try to subset the tree in case we want to check some
#target species
#check names of tips to use in sample subset
head(snake.tree$tip.label)

#make a subset of the tree and highlight a species
#levels back represents cladistic level (family, superfamily, order, class etc.)
snake.treeub<-tree_subset(snake.tree, "Hydrophis_viperinus", levels_back = 2)
snake.treeub %>% 
  ggtree(aes(color = group)) + 
  geom_tiplab(size=2) +
  theme_tree2() + 
  scale_color_manual(values = c(`1` = "red", `0` = "black")) +
  xlim(0, 80)

#break the tree into its basal parts as a tibble
tibtree <- as_tibble(snake.tree)

#remove that "_" from between the genera and specific epithet
tibtree$label <- sub("_", " ", tibtree$label)


#keep only the species, total body length, and ld50 data 
#we want in the "dat" data frame, have to divide for different trees
#or else the combination will produce NA and errors (i don't know why)
dat <- select(dat, Scientific.Name, IV..mgkg., TBL..cm.)


#change column names for joining
colnames(dat)[colnames(dat)=="Scientific.Name"] <- "label"
colnames(dat)[colnames(dat)=="IV..mgkg."] <- "LD50"
colnames(dat)[colnames(dat)=="TBL..cm."] <- "TBL"
dat$label<-as.character(dat$label)


#convert to tibbles for each type of trait
tibdat<-tibble(label=paste0(dat$label),
                   LD50=dat$LD50, TBL=dat$TBL)


library(stringr)
#remove any invisible characters (for some reason this happens)
tibdat$label<-str_replace_all(tibdat$label, "[^[:alnum:]]", " ")
tibtree$label<-str_replace_all(tibtree$label, "[^[:alnum:]]", " ")
#remove leading/trailing spaces from the data
#returns string w/o leading or trailing whitespace
trim <- function (x) gsub("^\\s+|\\s+$", "", x)

tibdat$label<-trim(tibdat$label)
tibtree$label<-trim(tibtree$label)

#add traits to the tree tibble we just made and merge using 
#scientific name column "label"
tib_tree <- full_join(tibtree, tibdat, by.x = "label")


#reclassify the tibble columns again (annoying but necessary)
tib_tree$parent<-as.integer(tib_tree$parent)
tib_tree$node<-as.integer(tib_tree$node)
tib_tree <- tib_tree[c("parent","node","branch.length","label","LD50", "TBL")]
#make sure everything is good for conversion
tib_tree
class(tib_tree)

#remove duplicates (in case there are any)
tib_treeND<-unique(tib_tree)

#convert into phylo object with trait data as a feature
new.snake.tree<-as.treedata(tib_treeND)

#check names to use for subset
new.snake.tree@phylo$tip.label

#subset the tree data (ignore the warning)
#if you try to plot the whole tree it won't work, I'm still unsure why that is 
treesub_new<-tree_subset(new.snake.tree, "Crotalus scutulatus", levels_back = 3)

#plot the tree with LD50 values as colors on the branches
ggtree(treesub_new, aes(color=LD50),
       ladderize = TRUE,right = FALSE, 
       continuous = FALSE, size=1) +
  scale_color_distiller(palette = "Reds", direction = 1) +
  geom_tiplab(hjust = -.1, size=1.8, color = "black") + 
  geom_nodelab(aes(x=branch), size=2.5, vjust=-0.5)+
  geom_tippoint() +
  theme(legend.position = c(0.80, .85))+
  xlim(0,70) 

#plot a tree with Total Body Length (TBL) on the branches
ggtree(treesub_new, aes(color=TBL),
       ladderize = TRUE,right = FALSE, 
       continuous = FALSE, size=1) +
  scale_color_distiller(palette = "Reds", direction = 1) +
  geom_tiplab(hjust = -.1, size=1.8, color = "black") + 
  geom_nodelab(aes(x=branch), size=2.5, vjust=-0.5)+
  geom_tippoint() +
  theme(legend.position = c(0.80, .85))+
  xlim(0,70)

#resub and do a sidebyside to see if you can visualize any correlations
#also lets change the species to some Hydrophis for a smaller subset
treesub_new<-tree_subset(new.snake.tree, "Hydrophis viperinus", levels_back = 2)

#plot the tree with LD50 values as colors on the branches
p1<-ggtree(treesub_new, aes(color=LD50),
       ladderize = TRUE,right = FALSE, 
       continuous = FALSE, size=1) +
  scale_color_distiller(palette = "Reds", direction = 1) +
  geom_tiplab(hjust = -.1, size=2.5, color = "black") + 
  geom_nodelab(aes(x=branch), size=2.5, vjust=-0.5)+
  geom_tippoint() +
  theme(legend.position = c(0.90, .85))+
  xlim(0,70) 

#plot a tree with Total Body Length (TBL) on the branches
p2<-ggtree(treesub_new, aes(color=TBL),
       ladderize = TRUE,right = FALSE, 
       continuous = FALSE, size=1) +
  scale_color_distiller(palette = "Reds", direction = 1) +
  geom_tiplab(hjust = -.1, size=2.5, color = "black") + 
  geom_nodelab(aes(x=branch), size=2.5, vjust=-0.5)+
  geom_tippoint() +
  theme(legend.position = c(0.90, .85))+
  xlim(0,70)

library(cowplot)
#side by side to check any correlation
plot_grid(p1, p2, ncol = 2, nrow = 1, labels = c("LD50", "TBL"))

R Code for this tutorial

making_trees_withr.r
File Size:	7 kb
File Type:	r

Download File

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Author

Russell J. Gray