What is Spatial Factor Interaction?¶
Spatial factor interaction lets you isolate, highlight, and compare specific factors of interest on both the spatial map and the UMAP coordinates rather than showing all factors overlaid at once in categorical colors.
Action Options
| Option | Double-Click (Pinned) | Hover (Preview) |
|---|---|---|
| Trigger | Double-click a factor chip in the drawer. | Move your cursor over a factor chip. |
| Limit to one factor | No. | Yes. |
| Persistence | Stays active until manually toggled off, reset, or a new layer is loaded. | Clears instantly when the cursor moves away. |
| Best For | Stable comparisons, capturing screenshots, or preparing data exports. | Rapidly scanning through factors to identify patterns. |
Visualization Options
| Option | Heatmap Mode | Flat Color Mode |
|---|---|---|
| Availability | Only for layers containing probability scores (e.g. HEX, or RAW_PIXEL with K2/K3). | Available for all vector-based factor layers. |
| Rendering | Continuous probability gradient (using the Turbo colormap). | Solid categorical color assigned to each factor. |
| Selection Limit | Yes. | No. |
| Background | Mute Background toggle hides unselected pixels or shows them at probability 0. |
Background Opacity and custom flat background color can be customized. |
| Best For | Visualizing cell density gradients or transition boundaries. | Comparing spatial boundaries of multiple cell types at a glance. |
What is selection limit?
Both Heatmap Mode and Hover interaction limit the selection to one factor at a time. So you can only highlight one factor if any of them are active.
Only when double-click action mode and flat color visulization mode are both enabled, you can highlight more factors simultaneously.
Why use spatial factor interaction?
- Spatial Localization: See exactly where a factor is located (e.g. mapping to a known anatomical layer or tissue region).
- Co-localization & Segregation: Compare multiple factors side-by-side to evaluate whether they overlap or occupy distinct spatial niches.
- UMAP Cross-Check: Correlate spatial localization with transcription clustering in the UMAP coordinates.
Related Pages
Concepts
Manual Pages
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