nodelabel.phylo: Blending information from taxonomies and trees

In mwpennell/geiger-v2: Analysis of Evolutionary Diversification

Blending information from taxonomies and trees

Description

working with systematic reference tables and phylogenies

Usage

nodelabel.phylo(phy, taxonomy, strict=TRUE, ncores=NULL)
phylo.lookup(taxonomy, ncores=NULL)
lookup.phylo(phy, taxonomy = NULL, clades = NULL, ncores=NULL)
phylo.clades(clades, phy=NULL, unplaced=TRUE, ncores=NULL)
glomogram.phylo(phy, subtrees)

Arguments

phy	a phylogenetic tree of class 'phylo' ('multiPhylo' in phylo.clades)
taxonomy	a linkage table (of class matrix) between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny
clades	a named list of clade definitions (i.e., spanning taxa; see Examples); spanning taxa may invoke other definitions found within the clades list
unplaced	whether to use 'unplaced' taxa if given as an element in clades
subtrees	a list of trees to be grafted into phy; each subtrees element must either be a 'phylo' or 'multiPhylo' object with branch lengths in the same units as phy (see Examples)
strict	whether to enforce strict labeling of nodes or allow liberal estimates of the best location of a given nodelabel
ncores	the maximum number of cores to be used

Details

nodelabel.phylo provides a function (as part of the phylo object returned) to resolve the hash key and node identifier for a label found in taxonomy. This function is the FUN element of the returned object. If the taxonomic label cannot be properly placed in the tree (i.e., no subtree is found that is absolutely consistent with the supplied taxonomy, the nearest matching node(s) will be returned when invoking FUN).

phylo.lookup converts a taxonomy into a phylogenetic tree.

lookup.phylo converts a phylogenetic tree (phy) into a linkage table based on nodelabels associated with phy, which can be supplemented with a taxonomy and (or) clades object.

phylo.clades returns a series of phylogenetic subtrees based on clade definitions found in the clades object. Definitions can be handles that are recursive (see Examples).

Author(s)

JM Eastman

Examples

## Not run: 
sal=get(data(caudata))
print(head(sal$tax))

## TREE from TABLE: phylo.lookup()
tax=cbind(sal$tax[,c("subfamily", "family", "suborder")], order="Caudata")
tphy=phylo.lookup(tax, ncores=2)
print(tphy)
head(tphy$node.label)

## TABLE from TREE: lookup.phylo()
tax=sal$tax[,c("genus", "family")]
cld=list(
	Sirenoidea=c("Siren", "Pseudobranchus"), 
	Salamandroidea=c("Ambystomatidae", "Plethodontidae"), 
	Cryptobranchoidea=c("Hynobius_naevius", "Cryptobranchus_alleganiensis"),
	CAUDATA=c("Sirenoidea","Salamandroidea","Cryptobranchoidea")
)
lkp=lookup.phylo(sal$phy, taxonomy=tax, clades=cld, ncores=2)
print(lkp)
nphy=nodelabel.phylo(sal$phy, lkp, ncores=2)
dev.new()
plot.phylo(ladderize(nphy,right=FALSE), cex=0.35, 
type="fan", label.offset=2.5, no.margin=TRUE, edge.color="gray", edge.width=0.5)

nodelabels(nphy$node.label, cex=0.45, col="red", frame="n")

## CLADES to TREE: phylo.clades()
fmrca=geiger:::.mrca
salamandroidea=extract.clade(nphy, fmrca(c("Ambystomatidae", "Plethodontidae"), nphy))
cryptobranchoidea=extract.clade(nphy, fmrca(c("Cryptobranchidae", "Hynobiidae"), nphy))
siren=extract.clade(nphy, fmrca(c("Siren_lacertina", "Siren_intermedia"), nphy))

clades=list(
			 Sirenoidea=c("Siren", "Pseudobranchus"), 
			 Caudata=c("Sirenoidea","Salamandroidea","Cryptobranchoidea"),
			 AMPHIBIA=c("Caudata","Anura","Gymnophiona")
)

phy=list(Cryptobranchoidea=cryptobranchoidea, Salamandroidea=salamandroidea, Siren=siren)
class(phy)="multiPhylo"

res=phylo.clades(clades, phy, ncores=2)
amph=nodelabel.phylo(res$AMPHIBIA, lkp, ncores=2)
print(amph$FUN("Salamandroidea"))
dev.new()
plot(ladderize(amph, right=FALSE), cex=0.2, label.offset=0.05)
nodelabels(amph$node.label, cex=0.35, col="red", frame="n")


## GLOMOGRAM
sirenidae=extract.clade(nphy, fmrca(c("Siren_lacertina", "Pseudobranchus_axanthus"), nphy))
ambystomatidae=extract.clade(nphy, fmrca(c("Ambystoma_gracile", "Ambystoma_texanum"), nphy))
trees=list(
	Cryptobranchoidea=cryptobranchoidea,
	Sirenidae=sirenidae,
	Ambystomatidae=ambystomatidae
)
class(trees)="multiPhylo"

fam=sal$fam
ftax=unique(sal$tax[,c("family", "suborder")])
rownames(ftax)=unname(ftax[,"family"])
fam=nodelabel.phylo(fam, ftax, ncores=2)
fam$FUN("Salamandroidea")

res=glomogram.phylo(fam, trees)
dev.new()
zz=match(res$tip.label, fam$tip.label)
cc=integer(length(zz))
cc[!is.na(zz)]=1

plot(ladderize(res, right=FALSE), cex=1, label.offset=5, tip.color=ifelse(cc==1, "red", "black"))

## End(Not run)

mwpennell/geiger-v2 documentation built on Feb. 26, 2023, 1:19 a.m.