R/exercise.R

In PhyloMeth/get-trees-jlampley: PhyloMeth exercises for getting trees from elsewhere

# Let's get some trees from Open Tree of Life. This is in some ways a
# successor to TreeBASE: another repository of trees (though it has only partial
# overlap with the trees in TreeBASE (or in another repository, Dryad). Unlike
# TreeBASE, anyone, not just the author, can add trees to Open Tree's 
# repository. Another important distinction is that Open Tree seeks to create
# a single tree for all life by creating essentially a supreme super tree.

GetTreeFromOpenTree_exercise <- function() {
	# Now let's look for the gecko genus Anolis
	# Figure out the id used for Anolis in Open Tree's database
 	# OTT: 5342306 this is the Open Tree ID for Anolis -jl
	# Replace the "__________" with appropriate arguments
	
	anolis.id <- tnrs_match_names("Anolis")$ott_id
	
	# Now get Open Tree's current best estimate of the phylogeny for the group
	# They call this the tree of life; we can get the subtree for just this group.
	anolis.tree <- tol_subtree(ott_id=anolis.id)
	
	# Let's plot the tree:
	plot.phylo(anolis.tree, type="fan", cex=0.2)
	
	# It has a lot of polytomies, representing uncertainty. A maximally resolved
	# tree (if rooted) will have one fewer internal nodes than terminal nodes:
	# think of a tree with three taxa, ((A,B),C): it'll have the MRCA of A and B
	# and the MRCA of A, B, and C: three terminals, two internal nodes. If it had
	# no information, it would only have one node. So we can look at the ratio of
	# number of internal nodes to number of possible internal nodes to figure out
	# how resolved a tree is (subtracting 1 from each to account for the root
	# node that must always exist)
	
	print(paste("The Anolis tree has ", Ntip(anolis.tree), " terminals and ", 
	Nnode(anolis.tree), " internal nodes out of ",Ntip(anolis.tree)-2,
	" possible, which means it is ", 
	round(100*(Nnode(anolis.tree)-1)/(Ntip(anolis.tree)-3), 2),
	"% resolved", sep=""))
	
	#Everything works up until this point.  There is something wrong with the rest
	#of this code - maybe a windows issue?? - jl.
	# Open Tree can also return the original studies with the source trees.
	anolis.studies <- studies_find_studies(property="ot:focalCladeOTTTaxonName",
	value="Anolis")
	anolis.studies.ids <- unlist(anolis.studies$study_ids)
	
	# Let's get info on the first study
	anolis.study1.metadata <- get_study_meta(anolis.studies.ids)
	print(get_publication(anolis.study1.metadata))
	
	# And let's get the tree from this study
	# Look in rotl documentation for the right function
	# Hint: get_study_trees() is close, but you don't know the tree.id
	anolis.study1.tree1 <- get_study(anolis.studies.ids)
	
	# And plot it
	plot.phylo(anolis.study1.tree1, type="fan", cex=0.2)
	
	#Return both trees
	return.list <- list(anolis.tree, anolis.study1.tree1)
	names(return.list) <- c("tol.tree", "study1.tree")
	return(return.list)
}