plot_orthotree: Create a phylogenetic tree of shared orthologs

In neurogenomics/orthogene: Interspecies gene mapping

Create a phylogenetic tree of shared orthologs

Description

Automatically creates a phylogenetic tree plot annotated with metadata describing how many orthologous genes each species shares with the reference_species ("human" by default).

Usage

plot_orthotree(
  tree = NULL,
  orth_report = NULL,
  species = NULL,
  method = c("babelgene", "homologene", "gprofiler"),
  tree_source = "timetree",
  non121_strategy = "drop_both_species",
  reference_species = "human",
  clades = list(Primates = c("Homo sapiens", "Macaca mulatta"), Eutherians =
    c("Homo sapiens", "Mus musculus", "Bos taurus"), Mammals = c("Homo sapiens",
    "Mus musculus", "Bos taurus", "Ornithorhynchus anatinus", "Monodelphis domestica"),
    Tetrapods = c("Homo sapiens", "Mus musculus", "Gallus gallus", "Anolis carolinensis",
    "Xenopus tropicalis"), Vertebrates = c("Homo sapiens", "Mus musculus",
    "Gallus gallus", "Anolis carolinensis", "Xenopus tropicalis", "Danio rerio"),
    Invertebrates = c("Drosophila melanogaster", 
     "Caenorhabditis elegans")),
  clades_rotate = list(),
  scaling_factor = NULL,
  show_plot = TRUE,
  save_paths = c(tempfile(fileext = ".ggtree.pdf"), tempfile(fileext = ".ggtree.png")),
  width = 15,
  height = width,
  mc.cores = 1,
  verbose = TRUE
)

Arguments

tree	A phylogenetic tree of class phylo. If no tree is provided (NULL) a 100-way multiz tree will be imported from UCSC Genome Browser.
orth_report	An ortholog report from one or more species generated by report_orthologs.
species	Species to include in the final plot. If NULL, then all species from the given database (method) will be included (via map_species), so long as they also exist in the tree.
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.
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.
non121_strategy	How to handle genes that don't have 1:1 mappings between input_species:output_species. Options include: "drop_both_species" or "dbs" or 1 : Drop genes that have duplicate mappings in either the input_species or output_species (DEFAULT). "drop_input_species" or "dis" or 2 : Only drop genes that have duplicate mappings in the input_species. "drop_output_species" or "dos" or 3 : Only drop genes that have duplicate mappings in the output_species. "keep_both_species" or "kbs" or 4 : Keep all genes regardless of whether they have duplicate mappings in either species. "keep_popular" or "kp" or 5 : Return only the most "popular" interspecies ortholog mappings. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. "sum","mean","median","min" or "max" : When gene_df is a matrix and gene_output="rownames", these options will aggregate many-to-one gene mappings (input_species-to-output_species) after dropping any duplicate genes in the output_species.
reference_species	Reference species.
clades	A named list of clades each containing a character vector of species used to define the respective clade using MRCA.
clades_rotate	A list of clades to rotate (via rotate), each containing a character vector of species used to define the respective clade using MRCA.
scaling_factor	How much to scale y-axis parameters (e.g. offset) by.
show_plot	Whether to print the final tree plot.
save_paths	Paths to save plot to.
width	Saved plot width.
height	Saved plot height.
mc.cores	Number of cores to parallelise different steps with.
verbose	Print messages.

Value

A list containing:

• plot : Annotated ggtree object.

• tree : The pruned, standardised phylogenetic tree used in the plot.

• orth_report : Ortholog reports for each species against the reference_species.

• metadata : Metadata used in the plot, including silhouette PNG ids from phylopic.

• clades : Metadata used for highlighting clades.

• method : method used.

• reference_species : reference_species used.

• save_paths : save_paths to plot.

Source

ggtree tutorial

Examples

orthotree <- plot_orthotree(species = c("human","monkey","mouse"))

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