load_tol: Load the Tree of Life or another file from ToL.

In barnabywalker/kewr: R Package to Access Kew Data APIs

Load the Tree of Life or another file from ToL.

Description

Request a tree file for the whole ToL or an alignment, sequence, or gene tree for a particular specimen or gene.

Usage

load_tol(url = NULL, .wait = 0.1)

Arguments

url	URL pointing to a file on the ToL SFTP server.
.wait	Time to wait before making a request, to help rate limiting.

Details

The Tree of Life is a database of specimens sequenced as part of Kew's efforts to build a comprehensive evolutionary tree of life for flowering plants.

Newick tree, alignment, and sequence files are help on an SFTP server for download. The URLs to access these are stored in entries for specimens and genes in the ToL database. These can be accessed by either using search_tol() to get all specimens for a particular order, family, genus, or species or by looking up a specific specimen or gene using lookup_tol(). If no URL is specified, this will load the ToL tree.

References

Baker W.J., Bailey P., Barber V., Barker A., Bellot S., Bishop D., Botigue L.R., Brewer G., Carruthers T., Clarkson J.J., Cook J., Cowan R.S., Dodsworth S., Epitawalage N., Francoso E., Gallego B., Johnson M., Kim J.T., Leempoel K., Maurin O., McGinnie C., Pokorny L., Roy S., Stone M., Toledo E., Wickett N.J., Zuntini A.R., Eiserhardt W.L., Kersey P.J., Leitch I.J. & Forest F. 2021. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Systematic Biology, 2021; syab035, https://doi.org/10.1093/sysbio/syab035

See Also

• lookup_tol() to lookup information about a sequenced specimen using a valid ToL ID.

• search_tol() to search ToL using taxonomic info.

• download_tol() to save a file on the ToL SFTP server to file.

Other ToL functions: download_tol(), lookup_tol()

Examples

 # load the ToL
 load_tol()

 # load a specimen fasta file
 specimen_info <- lookup_tol("1296")
 load_tol(specimen_info$fasta_file_url)

 # load a gene alignment file
 gene_info <- lookup_tol("51", type="gene")
 load_tol(gene_info$alignment_file_url)

 # load the gene tree
 load_tol(gene_info$tree_file_url)

barnabywalker/kewr documentation built on July 5, 2022, 5:37 p.m.