TX_wastewater_virome

Purpose

To share code and collaborate on analyses for the TEPHI wastewater virome manuscript (May 2022 - Feb 2023 data, Houston & El Paso)

How to get data

After cloning this repo, change to the repo directory, then:

wget https://zenodo.org/record/7884454/files/data.zip

unzip data.zip

The data files should now be in a directory called "data".

Using renv to load the versioned libraries and run analyses in RStudio

1. If not done already, git clone this repo

2. In the Finder, double click on TX_wastewater_virome.Rproj to load the project in RStudio

3. use renv to install the necessary libraries

renv::restore()

Running the analyses

With the data downloaded and the appropriate R packages downloaded, any of the .rmd files can be opened in R Studio.

Feel free to run the scripts in their entirety or chunk-by-chunk to reproduct the analyses.

Directory Tree

** There is a .gitignore on the data/ directory **

TX_wastewater_virome/
│   README.md
│   TX_wastewater_virome.Rproj
│
└───scripts/
│   └───virome_community/
│       │   some_scripts.Rmd
│   └───virus_variant_analyses/
│       │   some_scripts.Rmd
│   └───clinical_correlations/
│       │   some_scripts.Rmd
│   └───maps/
│       │   some_scripts.Rmd
│
└───data/
│   │   virus_abundance_table.tsv
│   │   WWTP_sample_metadata.xlsx
│   │   other_data.xlsx
│   │   etc
│
└───charts/
│   │   various_figures.pdf
│
└───environment/
    │   readme.md with package versions