Code for: Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora

By Isabelle Du Plessis, Hannah Snyder, Marian Dominguez-Mirazo, 2025

General Description

In this repository you can find all code needed to replicate the figures and analyses shown in the paper. All code is written in R v4.3.

Dependencies and package versioning

• ggplot2 v3.4
• reshape2 v1.4
• stats v4.3
• vegan v2.5
• grid v4.0
• gridExtra v2.3
• pracma v2.4
• ggpattern v1.0
• ggpubr v0.6
• dplyr v1.1
• GGally v2.1.2
• tidyverse v2
• readr v2.1

./IntermediateFiles

Contains files obtained from the analysis pipeline described in the manuscript and required to replicate figures.

• vOTUs.fasta : Sequences in fasta format for the vOTUs recovered in this study.

• votus_cov75thres_1224.txt : Read mapping information from reads from each sample to our vOTUs database.

• metadata.csv : Sample metadata including information as sample ID, location, year, root compartment, plant phenotype, ammong others.

• nullmodel.txt : Null model of vOTUs distribution, required for Figure 2, and generated by script: ~/Scripts/Fig2_NullModel/

• c1.ntw : Network output from vCONTACT2. This file is too large to store in github, and can be found in the associated zenodo repository.

• PIGEON_v1_habitat_origin.csv : Information on sample habitat for PIGEON v1 database, required for Figure 3. This file is too large to store in github, and can be found in the associated zenodo repository.

• relevant_clusters.list : Relevant cluster list, made up by vCONTACT2 clusters that include a vOTUs identified in our study. Required for Figure 3.

• hostPrediction_0225.tsv : Host predictions for vOTUs in this study derived from iPHOP.

• hostProperties_0225.tsv : Biogeochemical host properties associated to order level.

./ Scripts

Scripts in this folder generate the corresponding figure of the same name and store it in the ~/Figures folder.

• Fig1.R : Code for Figure 1 panels B,C,D.

• Fig2_NullModel : Generates null model of vOTU coocurrence distribution across plant phenotype/compartment combinations based on per combination vOTU abundance.

• Fig2_StatTest : Statistical tests for Figure 2.

• Fig2.R : Code for Figure 2, all panels.

• Fig3.R : Code for Figure 3.

• Fig4.R : Code for Figure 4.

./Figures

All manuscript figures, generated from scripts in ~/Scripts folder.

Zenodo associated link: https://doi.org/10.5281/zenodo.15102500