| BoSSA-package {BoSSA} | R Documentation |
Reads and plots phylogenetic placements.
The DESCRIPTION file:
| Package: | BoSSA |
| Type: | Package |
| Title: | A Bunch of Structure and Sequence Analysis |
| Version: | 3.7 |
| Date: | 2020-10-16 |
| Author: | Pierre Lefeuvre |
| Maintainer: | Pierre Lefeuvre <pierre.lefeuvre@cirad.fr> |
| Depends: | R (>= 3.3.0) |
| Imports: | ape, RSQLite, jsonlite, phangorn, plotrix |
| Suggests: | prettydoc, knitr, rmarkdown, XML, rentrez, httr |
| VignetteBuilder: | knitr |
| Description: | Reads and plots phylogenetic placements. |
| License: | GPL |
Index of help topics:
BoSSA-package A Bunch of Structure and Sequence Analysis
circular_tree Plot an inside-out circular tree
plot.pplace Plot a pplace or jplace object
pplace A placement object as obtained with the
read_sqlite function
pplace_to_matrix Pplace to contingency matrix
pplace_to_table Merge the multiclass and the placement table of
pplace object
pplace_to_taxonomy Convert a pplace object to a taxonomy table
print.pplace Compact display of pplace and jplace objects
print.protdb Compact display of protdb object
read_jplace Read a jplace file
read_protdb Read Protein Data Bank (PDB) file
read_sqlite Read a pplacer/guppy sqlite file
refpkg Summary data and plots for reference packages
sub_pplace Subsets a pplace object
write_jplace Write a jplace or pplace object to the disk
BoSSA contains functions to read and plot phylogenetic placement files obtained using softwares such as pplacer, guppy, EPA and RAPPAS.
Pierre Lefeuvre Maintainer: Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>
- pplacer and guppy http://matsen.fhcrc.org/pplacer/ http://matsen.github.io/pplacer/ - EPA https://sco.h-its.org/exelixis/web/software/epa/index.html - RAPPAS https://github.com/benclaff/RAPPAS - Common file format http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009