AWI-Gen Microbiome Pilot: Metagenomics

Analysis scripts for Wits-Stanford shotgun microbiome data.

To generate all figures from the manuscript, please follow these steps:

1. Clone this repo

2. Access phenotype and medication data from EGA under dataset ID EGAD00001006581. You can submit an access request to the H3Africa Data Access Committee at https://catalog.h3africa.org

3. Edit scripts/create_metadata.R to point to the locations of the EGA phenotype and medication data and run this script to create the required RData file

4. Install all required packages and run R scripts in scripts/figures, scripts/figures/supplementary, and nanopore/scripts

   e.g. from the command line:

      find scripts/figures -name "*.R" | xargs -I foo Rscript foo
   

Required packages for figures:

• DESeq2
• MASS
• Maaslin2
• RColorBrewer
• cowplot
• dplyr
• genefilter
• ggplot2
• ggpubr
• ggrepel
• gplots
• gtools
• harrietr
• here
• metagenomeSeq
• reshape2
• scales
• tidyverse
• vegan

Optional packages to reproduce map figure from Supplementary Information (scripts/figures/supplementary/supp_info_map.R)

• ggspatial
• maps
• rgeos
• rnaturalearth
• rnaturalearthdata
• sf