🔴 IMPORTANT note❗ (3th of April 2024)🔴
For the seasonality calculations, I used the lomb version 1.1.
As of today, there is the version 2.1, and the maximum peak at the yearly period is calculated differently.
I have changed the code accordingly from peak >= 10 to peak >= 0.154.
Author: Adrià Auladell
Inside src there are all the scripts with the following structure:
src/
data/ # processing of raw files with DADA2 + phyloseq
analysis/ # all the analysis generating new data or statistics
figures/ # the visualizations, mainly through ggplot
utils/ # scripts called from the abovementioned scripts
Inside the data/cleaned folder there is a phyloseq R object with the sequence data, abundance table and sample metadata.
To execute most of the analysis, create an R project in the main folder and execute the desired scripts. Most of the figures scripts
require to have executed scripts in the analysis folder for the statistics to be saved in the correspondent folders.
You will need some minimal packages for running the scripts. For most analysis:
- tidyverse: data wrangling, visualization and general purpose package.
- phyloseq: specific microbiome experiment functions.
- speedyseq: faster processes.
- propr: proportionality calculation.
- lomb: seasonality testing.
- DECIPHER: nucelotide calculations.
Regretabbly, there are also tons of other packages that I used for small processes. Sorry for that. Package-addict here :^/
Some of there are: janitor, geofacet, patchwork, gt, ggthemes, ggtext, ggraph....
If there is an issue dealing with the code or something else either post an issue in the project or write an email to [email protected] :)