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BeCrop® Portal Tools: The Co-Occurrence Tool

The Co-Occurrence Tool helps you analyze which microorganisms are shared or unique across groups of samples. It creates a Venn diagram that shows overlaps and differences between clusters, letting you explore microbial community patterns at a glance.

This tool is ideal for:

  • Identifying species common to all your samples

  • Finding organisms unique to certain parcels or treatments

  • Comparing biodiversity across different management practices

 

Accessing the Co-Occurrence Tool

  1. Log into your BeCrop® Portal.

  2. From the left-hand menu, go to Toolbox.

  3. Select Co-Occurrence Tool.

 

Setting Up Clusters

Just like in the HeatMap and BoxPlot tools, you’ll first need to group your samples into clusters:

  1. Select samples – Use the arrow or circle under each sample to assign it to a cluster.

  2. Name clusters – Give each group a clear label (e.g., “Biodynamic parcels” vs. “Conventional parcels”).

  3. Save clusters – Use the disk icon to save your configuration for future use.

  4. Load saved clusters – Access your saved configurations anytime using Load Saved Configurations.

 

Running a Comparison

Once your clusters are set, click Compare.



  1. The tool will generate a Venn diagram showing:

    • Shared organisms – Microorganisms present in multiple clusters

    • Unique organisms – Microorganisms found only in one cluster

  2. Hover over sections of the diagram to see the number of microorganisms represented.

 

Understanding Results

Key Metrics

  • Uniqueness – Organisms found in some samples of a cluster but absent from all other clusters.

  • Species Richness – The variety of organisms within each cluster.

  • Cluster Uniqueness – Organisms consistently found in all samples of a cluster, but not in others.

  • Commonality – Organisms that are common across clusters.

Drill Down into Lists

  • Click on colored bars to expand the list of species.

  • Use the search bar to quickly locate a specific microorganism (e.g., Lachancea thermotolerans).

Example Questions You Can Answer

  • Do my biodynamic parcels host species absent from conventional parcels?

  • Is Lachancea thermotolerans common across all my vineyard blocks?

  • How many microorganisms were shared between last month’s samples?

When to Use the Co-Occurrence Tool

  • To compare microbial diversity across management styles (e.g., organic vs. conventional)

  • To identify unique organisms tied to a specific field or treatment

  • To understand overlaps in microbial communities across clusters of samples

👉 Want a Step-by-Step Walkthrough?

Prefer to learn by watching? Check out our explainer video on using the Co-Occurrence Tool for a guided, step-by-step demo.