Prepare a phylogenetic tree

Source: R/prepare_tree.R

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.

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).

Examples

species <- c("human","chimp","mouse")
tr <- orthogene::prepare_tree(species = species)
#> Importing tree from: TimeTree2022
#> Importing cached tree.
#> Standardising tip labels.
#> Mapping 3 species from `species`.
#> Mapping 3 species from tree.
#> --
#> 0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`.
#> --
#> 0/3 (0%) tips dropped from tree according to overlap with selected `species`.