brranching tutorial

for v0.2.0

R client to fetch phylogenies from many places. Right now we only fetch phylogenies from Phylomatic, but we'd like to add more sources down the road.

Installation

Install and load brranching into the R session. Stable version from CRAN

install.packages("brranching")

Or development version from Github:

install.packages("devtools")
devtools::install_github("ropensci/brranching")
library('brranching')

Usage

Phylomatic

Use the web service

taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
tree <- phylomatic(taxa = taxa, get = 'POST')
plot(tree, no.margin = TRUE)

You can pass in up to about 5000 names. We can use taxize to get a random set of plant species names.

library("taxize")
spp <- names_list("species", 200)
out <- phylomatic(taxa = spp, get = "POST")
plot(out, show.tip.label = FALSE)

Use Phylomatic locally

Phylomatic is written in Awk, and the code can be downloaded to run locally on your own machine. This approach is for the more adventurous user. The benefit of using Phylomatic locally is that you can run larger set of names through - when using the web service it has a maximum number of taxa it will take in as the maintainer does not want any one person taking up a large amount of server capacity.

First, download the code by doing git clone https://github.com/camwebb/phylomatic-ws, which will result in a folder phylomatic-ws (or download a zip file, and uncompress it). Then give the path to that folder in the path parameter in the phylomatic_local() function as show below.

taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
(tree <- phylomatic_local(taxa, path = "~/github/play/phylomatic-ws"))
#> 
#> Phylogenetic tree with 3 tips and 2 internal nodes.
#> 
#> Tip labels:
#> [1] "poa_annua"         "phlox_diffusa"     "helianthus_annuus"
#> Node labels:
#> [1] "poales_to_asterales"   "ericales_to_asterales"
#> 
#> Rooted; no branch lengths.

Note how the path ~/github/play/phylomatic-ws is specific to a computer - Change it to for your computer.

Then we can plot just as above using the phylomatic() function

plot(tree, no.margin = TRUE)

Citing

To cite brranching in publications use:


Scott Chamberlain (2016). brranching: Fetch 'Phylogenies' from Many Sources. R package version 0.2.0. https://github.com/ropensci/brranching

License and bugs

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