In trvinh/taxFun: taxFun

knitr::opts_chunk$set(
    library(taxFun),
    collapse = TRUE,
    comment = "#>",
    dev = 'png',
    crop = NULL
)

Introduction

WRITE SOMETHING HERE

How to install taxFun

if (!requireNamespace("devtools"))
    install.packages("devtools")
devtools::install_github("trvinh/taxFun", INSTALL_opts = c('--no-lock'), build_vignettes = TRUE)

Input and output

A text file containing list of taaxon IDs or names or a mix of them. For example:

Homo sapiens
100226
10090
10116
1111708
Xenopus tropicalis
122586
13616
164328
184922

taxFun will return the result in a (tab-delimited) text file. If not specified in the command, output file will be saved as input.* by default.

Features and capabilities

| Function name | Main input | Output | Other options | |---|---|---|---| | getAllTaxonomyRanks | None | A list of all available NCBI taxonomy ranks | None | | id2name | List of taxon IDs | A table containing input taxon IDs and their scientific names | None | | name2id | List of taxon names | A table containing input taxon names and their taxon IDs | None | | getRank | List of taxon IDs or/and names | A table containing input taxa and their taxonomy ranks | None | | getRanks | List of taxon IDs or/and names | A table containing input taxon IDs, their scientific names and the names of selected taxonomy ranks | ranks = list of selected taxonomy ranks (Optional: if not given, all possible taxonomy ranks will be considered) | | sortTaxonomyMatrix | List of taxon IDs or/and names | A clustered taxonomy matrix, shorted by a selected reference species | refspec = specified reference species | | createTree | List of taxon IDs or/and names | Tree file in newick format | outgroup = outgroup species for rooting (Optional) | | getRepresentative | List of taxon IDs or/and names | A table containing list of sub-selected taxa and their taxonomy info | rank = selected rank used for sub-sampling. Each supertaxon of this rank will have one representative | | getClade | List of taxon IDs or/and names | Subset of taxa that belong to a specified taxonomy clade | supertaxon = clade ID or name | | getLCA | List of taxon IDs or/and names | Last common ancestor name and ID | None |

Examples

# specify list of taxon IDs or taxon names
idFile <- system.file(
    "extdata", "ids.txt", package = "taxFun", mustWork = TRUE
)
nameFile <- system.file(
    "extdata", "names.txt", package = "taxFun", mustWork = TRUE
)

# convert IDs to names
taxFun("id2name", idFile)

# get names of class, family and phylum for a list of given taxon names
taxFun("getRanks", nameFile, ranks = c("class", "family", "phylum"))

# create an aligned taxonomy hierarchies for a list of taxon IDs
taxFun("sortTaxonomyMatrix", idFile, refspec = "Homo sapiens")

# create taxonomy tree rooted by an outgroup species
taxFun("createTree", nameFile, outgroup = "Homo sapiens")

# sub-sample taxa on phylum level
taxFun("getRepresentative", idFile, rank = "phylum")

# get all metazoa species
taxFun("getClade", idFile, supertaxon = "metazoa")

# get last common ancestor
taxFun("getLCA", nameFile)

More examples? Please tell us what you want to see ;-)

How to cite

Ngoc-Vinh Tran, Bastian Greshake Tzovaras, Ingo Ebersberger, PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages 3041–3043, https://doi.org/10.1093/bioinformatics/bty225

Or use the citation function in R CMD to have the citation in BibTex or LaTeX format

citation("taxFun")

How to contribute

Thank you so much for your interest in contributing to taxFun! 🎉👍🍾

Contributions to taxFun can take many forms. If you are

biologist, you can report bugs, tell us about what features you would love to see, improve our documentation, both in the Wiki and in our README, discuss about non-coding issues

biologist and love coding, you can fix existing bugs, or add new features, or basically whatever great idea you have! and all points for non-coding contributors as well :)

not biologist but can code, it would be great if you can test the tool in different environments (Windows, Linux, Mac - Firefox, Chrome, IE, Safari,...) suggest a better user interface * improve the code quality

Don't hesitate to get in touch with us if you have any questions. You can contact us at [e-mail]

Contributors {.unnumbered}

• Vinh Tran

SessionInfo()

Here is the output of sessionInfo() on the system on which this document was compiles:

sessionInfo(package = "taxFun")

References

trvinh/taxFun documentation built on July 3, 2023, 8:55 p.m.