Co-occurrence Matrix
The co-occurrence matrix reveals hidden patterns across your notes by analyzing how strongly they relate to each other. It's the same relationship data as the graph, shown as a grid.
Reading the Matrix
The matrix is a heatmap:
- Each row and column is a note or node
- Each cell is the relationship between that pair; deeper blue means a stronger connection (measured by Jaccard similarity — how much two notes' link neighborhoods overlap)
- Empty/neutral cells mean little or no relationship
The color language is consistent across the whole app: deeper blue = stronger, in both the matrix and the graph, so switching between them needs no relearning.
Clusters and Structure
Jotaid groups related notes automatically and draws them out visually:
- Clusters — bright blocks along the diagonal are groups of notes that belong together; bracket markers show cluster boundaries
- Bridge notes — notes that connect otherwise separate clusters
- Isolated notes — notes with few connections that might need linking
How to Use It
- Open Node view and switch to the Matrix tab
- On iOS, use the bottom capsule to toggle between Graph and Matrix
- Hover (macOS) or tap (iOS) a cell to see the pair's relationship details
- Follow a bright cell to the two notes behind it and consider linking or merging them
TIP
The matrix earns its keep once you have 10+ notes with backlinks — the more you link, the more patterns emerge. With Pro, AI can explain a strong relationship in plain language, turning a bright cell into a sentence.
Next Steps
- Backlinks & Graph — The graph view of the same data
- AI Workflows — Let AI interpret the patterns