Tutorial: Exploring M2M-PostAViz with Example Data

This tutorial demonstrates how to use M2M-PostAViz with the built-in test dataset. You will learn how to launch the application, navigate its main features, and interpret the results.

Prerequisites

  • M2M-PostAViz is installed (see Installation)

  • You have access to a terminal or command prompt

Step 1: Launch the Application with Test Data

Run the following command in your terminal:

m2m_postaviz --test

  • This will extract and process example data from the postaviz_test_data directory.

  • The process may take a few seconds.

  • The Shiny web application will open automatically in your browser.

Step 2: Overview Tab

  • What you see: Summary statistics: number of metabolic networks, samples, and unique metabolites.

  • Plots: - Number of unique metabolites per sample - Total number of compounds reached - Principal Coordinate Analysis (PCoA) plots

Homepage of PostaViz

  • Try: - Grouping samples by metadata variables - Exporting data frames and plots

Overview exploration tab

Step 3: Taxonomy-based Exploration Tab

  • Purpose: Explore metabolic potential by taxonomic groups or individual genomes.

  • Actions: - Select taxonomic rank (e.g., phylum, genus) - Filter samples by metadata - Enable abundance weighting

  • Plots: - Number of metabolites produced by selected taxa (individual and community metabolic potentials) - Relative abundance of selected taxa in samples

Taxonomy-based exploration tab

Step 4: Metabolite-based Exploration Tab

  • Purpose: Explore the production of specific metabolites or compound families.

  • Actions: - Select compounds (Metacyc data is not available with the test data) - Filter and group samples by metadata - Enable clustering for heatmaps depicting the number of producers for each metabolites by groups.

  • Plots: - Heatmaps of compound production - Percentage of samples producing selected compounds - Boxplots grouped by metadata

Metabolite-based exploration tab

Step 5: Metadata Management Tab

  • Purpose: Review and edit metadata types for your variables.

  • Actions: - Change variable types (categorical, numeric, etc.) - See how changes affect plots and analyses

Step 6: Exporting Results

  • Export: - Try downloading data frames, plots, and statistical results from each tab for further analysis.

Tips and Notes

  • The test dataset is small and designed for demonstration purposes.

  • For your own data, see Input Data and Usage.

  • Some features (e.g., Metacyc ontology) are not available in this mode.

Next Steps

  • Try running M2M-PostAViz with your own data generated with Metage2Metabo.

  • Explore advanced options and custom analyses.