sw1/theseus

R pkg for analysis, visualization, and interpretation of community composition data

Overview

theseus provides functions to assist in the analysis, visualization, and interpretation of community composition data, especially those originating from amplicon sequencing.

Relevant Software and Literature

Callahan, Sankaran, Fukuyama, McMurdie, and Holmes (2017) Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data Oksanen,Blanchet, Friendly, Kindt, Legendre, McGlinn, Minchin, O'Hara, Simpson, Solymos, Stevens, Szoecs, and Wagner (2017) vegan: Community Ecology Package

Installation

# To install the release version of theseus:
install.packages('theseus')

# To install the developmental version via Github:
# install.packages('devtools')
devtools::install_github('sw1/theseus',build_vignettes=TRUE)

Development

For future feature requests or suggestions, request an issue:

https://github.com/sw1/theseus/issues

theseus's Issues

Theseus p.prev error

Hi there. Was curious about using this package but encountered some errors. It seems that formatting of the phyloseq files between your example data, and my own are not the same:

It looks like at the OTU_Table level our samples and reference names are swapped which then results in this error:

p.prev <- prev(RAB_fungi, taxon="Order", n_taxa=5)
Error in data.frame(tax = phyloseq::taxa_names(PS), abundance = phyloseq::taxa_sums(PS), :
arguments imply differing number of rows: 2502, 102

Any suggestions?