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taxtree

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1.0.0

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taxtree

Overview

The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet. The official address for the NCBI Taxonomy database is https://www.ncbi.nlm.nih.gov/taxonomy and the public data download address is https://ftp.ncbi.nih.gov/pub/taxonomy/. taxtree is used to generate a a phylogenetic topology of taxonomic units (taxa) based on the Taxonomy database by processing names.dmp and nodes.dmp and drawing simple evolutionary trees based on the hierarchy of taxa. The implementation of taxtree function relies on tidyverse and ggtree. Currently, taxtree allows 768,430 taxa from the taxonomy database to be used to construct the topology of a phylogenetic tree.

Ranks	higher taxa	genus	species	lower taxa	total
Archaea	610	264	878	0	1,752
Bacteria	5,897	5,005	24,761	952	36,615
Eukaryota	67,028	98,600	515,880	36,640	718,148
Fungi	6,009	7,437	55,840	1,571	70,857
Metazoa	48,564	70,320	270,261	18,292	407,437
Viruses	2,064	2,587	7,180	65	11,896
Bacteria	5,897	5,005	24,761	952	36,615
All taxa	75,630	106,458	548,685	37,657	768,430

Installation

Before installing, you will need to download the taxtree dependency package ggtree by BiocManager.

if (!require("BiocManager"))
  install.packages("BiocManager")
library(BiocManager)
if (!require("ggtree"))
  BiocManager::install("ggtree")

Install devtools, which is used to install R packages from GitHub.

if (!require("devtools"))
  install.packages("devtools")

Once you have completed the above steps, start the installation.

devtools::install_github("nongxinshengxin/taxtree")

Function

taxtree has six core functions.

make_Taxtree() If you have some definite taxa names (either Kingdom Phylum Class Order Family Genus Species or any other taxonomic node), you can use this function to construct their taxonomic topology from a list of taxa names.
find_Lineage() By an explicit taxon name, all taxonomic lineages under that taxno are found.
name2rank() If you have some definite taxa names (either Kingdom Phylum Class Order Family Genus Species or any other taxonomic node), you can use this function to get the taxonomy rank name (and taxid) based on the name of the taxa.
name2rank_str() If you have some definite taxa names (either Kingdom Phylum Class Order Family Genus Species or any other taxonomic node), you can use this function to get the taxonomy rank name (and taxid) based on the name of the taxa. You can input a single string or a vector containing multiple strings in this function.
plot_taxTree() Drawing a simple Taxonomy tree based on the ggtree package.
write_taxTree() This function writes in a file a tree in parenthetic format using the Newick format, based on ape packages.

Application

Species annotation based on OTUs, allowing the construction of their phylogenetic topology based on the names of taxa obtained from the annotation, using the make_Taxtree() function;
Conducting taxonomic studies. Curious about the close relatives of humans under the order Primates? find_Lineage("Primates") is a one-line command that will give you the answer;
Border Phylum Order Family Genus Species, classification is just too complicated. name2rank(), name2rank_str(), just provide the name of the taxa and it will tell you its taxonomic rank;
Super linkage. taxtree is based on the Taxonomy database and can be linked to TaxonKit software; also, taxtree generates S3 phylo classes, which are commonly used to store phylogenetic trees in R. The tree can be easily embellished in depth using the ggtree package. The tree can also be output via write_taxTree(), combined with the itol.toolkit package and embellished with iTOL.

Reference

Hadley Wickham. https://github.com/tidyverse/tidyverse

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628