Comau Fjord — Reproducibility Bundle

Seasonal microbial community dynamics in Comau Fjord, Patagonia (Chile).
MAG-based metagenomics, two depths (5 m, 20 m), three Southern Hemisphere seasons.

How to reproduce

1. Install dependencies (once)

Several packages come from Bioconductor (phyloseq, ggtree, treeio, ggtreeExtra) and cannot be installed with install.packages(). Run the provided installer first:

setwd("path/to/reproducibility")
source("install_packages.R")

2. Run figure scripts

Each script is self-contained and must be run from this directory:

source("Figure1_final.R")       # Fig. 1: Map, PCoA, phylum seasonality, aMPD
source("Figure2_final.R")       # Fig. 2: dbRDA, variance partitioning
source("Figure3_final.R")       # Fig. 3: Pathway sentinel analysis, eigengene PCoA
source("Figure4_final.R")       # Fig. 4: Circular family phylogeny + pathway heatmap
source("Figure5_final.R")       # Fig. 5: SES-MPD, SES-FDis, SES-CWSD panels
source("Distance–decay MRM.R")  # Supp: MRM distance-decay

All scripts call source("utils.R") automatically.
Figure3_final.R writes fig3_shared_objects.RDS (already included); Figures 4 and 5 read it.

Files

File	Description
utils.R	Shared palettes, season helper, load_ps() data loader
Comau_ps90.RDS	Primary phyloseq object — 90%-dereplicated MAGs, all samples
metadata.tsv	Sample metadata: coordinates, environmental variables, dates
gene_bin_mat.collapsed.v6.csv	DRAM functional annotation hit matrix (genes × MAGs, 677 MAGs)
fig3_shared_objects.RDS	Pre-computed abundance/hit matrices from Fig. 3 (used by Figs. 4 & 5)
CHL_adm_shp/	GADM Chile administrative shapefiles for the map panel

Key packages

phyloseq, vegan, ggplot2, dplyr, tidyr, patchwork, ARTool,
picante, ape, ecodist, geosphere, sf, rnaturalearth,
ggtree, ggtreeExtra, treeio, ggnewscale, scales