Salamander phylogeny of 44 species

#install.packages("phytools")
rm(list=ls())
library(phytools)

## Loading required package: ape

## Loading required package: maps

library(ape)
library(MASS)
library(stringr)
library(scales)
library(ggplot2) 
library(ggtree)

## ggtree v3.4.0 For help: https://yulab-smu.top/treedata-book/
## 
## If you use the ggtree package suite in published research, please cite
## the appropriate paper(s):
## 
## Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
## ggtree: an R package for visualization and annotation of phylogenetic
## trees with their covariates and other associated data. Methods in
## Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
## 
## S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
## Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
## visualization of richly annotated phylogenetic data. Molecular Biology
## and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166
## 
## LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR
## Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package
## for phylogenetic tree input and output with richly annotated and
## associated data. Molecular Biology and Evolution. 2020, 37(2):599-603.
## doi: 10.1093/molbev/msz240

## 
## Attaching package: 'ggtree'

## The following object is masked from 'package:ape':
## 
##     rotate

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following object is masked from 'package:MASS':
## 
##     select

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(httr)

tree<-read.tree("http://tonyjhwueng.info/phymvrates/ple.nwk")
tipl<-tree$tip.label
tree$tip.label<-str_replace_all(tree$tip.label,"Plethodon","P.")
plot(tree)

df<-read.csv("http://tonyjhwueng.info/phymvrates/Adams2012-SystBiolData.csv")
df$spname<-tree$tip.label
df$spname %in% tree$tip.label

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

tree$tip.label %in% df$spname  

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

df<-df[match(tree$tip.label, df$spname) ,] 
traitset<-df[,2:4]
rownames(traitset)<-tree$tip.label

dotTree(tree,traitset,standardize=FALSE,length=6,colors="orange")