Code for Plotting a Nice 78-Taxon Phylogeny with Stratigraphic Ranges, Upward Orientation, Phylopics, White Foreground Color with Black Background, etc

make_78taxon_phylopic_tree.R

devtools::install_github("dwbapst/paleotree", ref="dev_refinedphylopicfun")
library(paleotree)

taxaSeventyEight <- c(
	"Archaeopteryx", "Pinus", "Procoptodon", "Olenellus", "Eldredgeops",
	"Quetzalcoatlus", "Homo", "Tyrannosaurus", "Triceratops", "Giraffa",
	"Bolivina", "Cancer", "Dicellograptus", "Dunkleosteus", "Solanum",
	"Anomalocaris", "Climacograptus", "Halysites", "Cyrtograptus", 
	"Procoptodon", "Megacerops", "Moropus", "Dimetrodon", "Lingula",
	"Rhynchosaurus", "Equus", "Megaloceros", "Rhynchotrema", "Pecten",
	"Echinaster", "Eocooksonia", "Neospirifer", # "Prototaxites", 
	"Cincinnaticrinus", "Nemagraptus", "Monograptus", "Pongo", "Acropora",
	"Histiodella", "Agathiceras", "Juramaia", "Opabinia", "Arandaspis",
	"Corvus", "Plethodon", "Latimeria", "Phrynosoma", "Araucarioxylon",
	"Velociraptor", "Hylonomus", "Elginerpeton", "Rhyniognatha",
	"Tyto", "Dromaius", "Solenopsis", "Gorilla", "Ginkgo", "Terebratella", 
	"Caretta", "Crocodylus", "Rosa", "Prunus", "Lycopodium", "Meganeura",
	"Diplodocus", "Brachiosaurus", "Hepaticae", "Canadaspis", "Pikaia",
	"Smilodon", "Mammuthus", "Exaeretodon", "Redondasaurus", "Dimetrodon",
	"Megatheriidae", "Metasequoia", "Aedes", "Panthera", "Megalonyx")

data <-getSpecificTaxaPBDB(taxaSeventyEight)
tree <- makePBDBtaxonTree(data, rank = "genus") 

timeTree <- dateTaxonTreePBDB(tree,
  minBranchLen = 10)

file <- "tree_taxa78_03-15-19c.png"
png(file = file,
	height = 5, width = 12, 
	units = "in", res = 300)
par(bg="black")
par(mar=c(0,0,3,0))
taxaColors <- rep("white",Ntip(timeTree))
taxaColors[4] <- "red"
plotPhyloPicTree(
	tree = timeTree, 
	orientation = "upwards",
	addTaxonStratDurations = TRUE,
	edge.color = "white",
	maxAgeDepth = 700,
	taxaColor=taxaColors,
	depthAxisPhylo = TRUE,
	colorAxisPhylo = "white")
dev.off()
shell.exec(file)