Using rotl to create phylogenetic trees

dosullivan019 · June 12, 2021, 1:41pm

rOpenSci package or resource used*

What did you do?

Used rotl to create a phylogenetic tree using a species scientific name and included clipart for each animal using phylopic.

URL or code snippet for your use case*

github.com

dosullivan019/30DayChartChallenge/blob/e4f5fe3e9d6245a5a65b7d617c785781eaaa5b69/code/day16_tree.R

# 30 Day Chart challenge 2021
# 16th April 2021: Tree
# Data Source: rotl r package for Open Tree of Life
# Clipart using phylopic http://phylopic.org/
library(rotl)     # to get phylogenetic data
library(ggtree)   # to plot phylogenetic tree
library(ggplot2)
library(ggimage)  # needed for phylopic
library(extrafont)

# Define the species to look at and tnrs_match_names will find their id to use in creating tree
taxa <- tnrs_match_names(names = c("Ornithorhynchus anatinus", # platypus
                                   "Tachyglossus aculeatus",   # echidna
                                   "Phascolarctos cinereus",   # koala
                                   "Macropus giganteus",       # kangaroo   
                                   "Ailuropoda melanoleuca",   # panda
                                   "Carcharodon carcharias",   # great white
                                   "Megaptera novaeangliae",   # humpback
                                   "Eudyptula minor",          # little penguin
                                   "Tiliqua scincoides",       # blue tongue lizard

This file has been truncated. show original

Image

Sector

other

Twitter handle

@dosullivan019

Topic		Replies	Views
Linking phylogenetic and geographic data using rotl and rgbif UseCases rgbif , rotl	1	1852	March 22, 2019
preprint on rotl (R open tree of life) package Package Use Questions	4	1515	November 4, 2015
phylogram: dendrograms for evolutionary analysis Blog onboarding , phylogenetics , software	0	725	July 12, 2018
Use Phylomatic locally on your own machine from R UseCases r , phylogenetics , phylo	0	1693	December 13, 2016
treeio: Phylogenetic data integration Blog r , onboarding , phylogenetics , review	1	662	October 22, 2019

Using rotl to create phylogenetic trees

rOpenSci package or resource used*

What did you do?

URL or code snippet for your use case*

Image

Sector

Twitter handle

Related topics