run_ordination_analysis

A flexible ordination and PERMANOVA analysis pipeline for phyloseq objects, supporting custom grouping, interactions, and automatic sample filtering.

Ordination and PERMANOVA Pipeline

This function provides a flexible ordination and PERMANOVA analysis pipeline for phyloseq objects, supporting custom grouping, interactions, and automatic sample filtering. The pipeline is fully adaptable to any gene marker or community dataset.

How to Use

1. Download or Source the Function

You can source the R script directly from your local folder:

source("run_ordination_analysis.R")

OR from

source("https://raw.githubusercontent.com/mghotbi/run_ordination_analysis/Rhizosphere-nitrogen-fate/run_ordination_analysis.R")

# Load your normalized phyloseq object (ps_16s_norm) # normalization_set function in DspikeIn package

result <- run_ordination_analysis(
  ps_obj = ps_16s_norm,
  marker_label = "Prokaryotic Community",
  group_var = "Condition",
  interaction_var = "Wheat",
  replicate_var = "Replicate",
  treatment_levels = c("Optimum", "Drought", "Heat", "Drought+Heat"))

# View the plot and PERMANOVA
result$plot
result$permanova