prepare_tree: Prepare a phylogenetic tree

In neurogenomics/orthogene: Interspecies gene mapping

Prepare a phylogenetic tree

Description

Import a phylogenetic tree and then conduct a series of optional standardisation steps. Optionally, if output_format is not NULL, species names from both the tree and the species argument will first be standardised using map_species.

Usage

prepare_tree(
  tree_source = "timetree",
  species = NULL,
  output_format = "scientific_name_formatted",
  run_map_species = c(TRUE, TRUE),
  method = c("homologene", "gprofiler", "babelgene"),
  force_ultrametric = TRUE,
  age_max = NULL,
  show_plot = TRUE,
  save_dir = tools::R_user_dir("orthogene", which = "cache"),
  verbose = TRUE,
  ...
)

Arguments

tree_source	Can be one of the following: "timetree2022": Import and prune the TimeTree >147k species phylogenetic tree. Can also simply type "timetree". "timetree2015": Import and prune the TimeTree >50k species phylogenetic tree. "OmaDB": Construct a tree from OMA (Orthologous Matrix browser) via the getTaxonomy function. NOTE: Does not contain branch lengths, and therefore may have limited utility. "UCSC": Import and prune the UCSC 100-way alignment phylogenetic tree (hg38 version). "<path>": Read a tree from a newick text file from a local or remote URL using read.tree.
species	Species names to subset the tree by (after standardise_species step).
output_format	Which column to return.
run_map_species	Whether to first standardise species names with map_species.
method	R package to use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
force_ultrametric	Whether to force the tree to be ultrametric (i.e. make all tips the same date) using force.ultrametric.
age_max	Rescale the edges of the tree into units of millions of years (MY) instead than evolutionary rates (e.g. dN/dS ratios). Only used if age_max, the max number , is numeric. Times are computed using makeChronosCalib and chronos.
show_plot	Show a basic plot of the resulting tree.
save_dir	Directory to cache full tree in. Set to NULL to avoid using cache.
verbose	Print messages.
...	Additional arguments passed to makeChronosCalib.

Value

A filtered tree of class "phylo" (with standardised species names).

Source

TimeTree 5: An Expanded Resource for Species Divergence Times

Examples

species <- c("human","chimp","mouse")
tr <- orthogene::prepare_tree(species = species)

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.