recipe r-saccharis

A rendering package for creating phylogenetic trees from SACCHARIS .json and .tree files, in the R statistical computing language.

Homepage:

https://github.com/saccharis/rsaccharis

License:

GPL / GPL-3.0-or-later

Recipe:

/r-saccharis/meta.yaml

This package will use metadata .json and .tree files output from SACCHARIS v2 to generate annotated phylogenetic tree PDF files. Highly customizable, as the formatting of the tree is done using ggplot2. Of course plotting functions can easily be manipulated as desired. To use, call A_load_data() and B_plots_all() and follow prompts. Our default plots used for publication are domain_ECno_numeric.

package r-saccharis

(downloads) docker_r-saccharis

versions:

1.0.5-0

depends bioconductor-ggtree:

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggnewscale:

depends r-ggplot2:

depends r-jsonlite:

depends r-knitr:

depends r-magrittr:

depends r-rcolorbrewer:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-saccharis

and update with::

   mamba update r-saccharis

To create a new environment, run:

mamba create --name myenvname r-saccharis

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/r-saccharis:<tag>

(see `r-saccharis/tags`_ for valid values for ``<tag>``)

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Link to this page

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