Repository for data analyses scripts of Hu et al. (2019)
| Script Filename | Content |
|---|---|
| Heatmaps_and_Ordinations.R | main script for drawing multiple heatmaps and ordination plots |
| DataLoader.R | separate script to preload and wrangle the data for DE_testing.R (is included in Heatmaps_and_Ordinations.R) |
| DE_testing.R | DESeq2 differential abundance testing, knitr spin compatible |
All data was analyzed in R (v 3.6.1.). The following additional packages should be installed to run the provided code:
- ggplot2 (CRAN)
- extrafont (CRAN)
- phyloseq (BioConductor)
- NMF (CRAN)
- vegan (CRAN)
- gplots (CRAN)
- readxl (CRAN)
- DESeq2 (BioConductor)
- data.table (CRAN)
- splitstackshape (CRAN)
- dplyr (CRAN)
- scales (CRAN)
- ape (CRAN)