# Analysis and Visualization Tools for Microbial Community Data

## Documentation for package ‘theseus’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cohort_relabund | Creates a relative abundance cohort plot
constord | Plots constrained ordination results
envtoverlay | Environmental variable fitting to unconstrained ordination diagrams
prev | Create prevalence vs abundance plot
pstoveg_otu | converts the otu_table slot of a phyloseq object to a vegan-compatible matrix
pstoveg_sample | Converts sample_data slot of a phyloseq object to vegan-compatible matrix
pstoveg_sd | converts the sam_data slot of a phyloseq object to a vegan-compatible matrix
qualcontour | Create read quality color contour plots
sigtab | Differential abundance data
sigtab.2vs3 | Differential abundance data
WWTP_Impact | Freshwater stream microbiome data