Navigating the Scatterplot
The scatterplot is the main visualization area where proteins appear as points. Learn how to navigate, select, and explore your data.
Quick Reference
| Action | How |
|---|---|
| Zoom in/out | Mouse wheel or pinch gesture |
| Pan | Click + drag on background |
| Reset view | Double-click on background |
| Select one | Click a point |
| Add to selection | ⌘/Ctrl + click another point |
| Box select | Click Select button, then drag |
| Clear selection | Press Escape or click Clear |
| Exit selection mode | Press Escape (when no selection) |
| Focus search | ⌘/Ctrl + K |
Navigation
- Zoom: Scroll wheel or pinch gesture
- Pan: Click and drag on the background
- Reset: Double-click the scatterplot to fit all proteins
Selection
Single & Multi-Select
- Click a point to select it
- ⌘ + click (Mac) or Ctrl + click (Windows) to add to selection
- Click the same point again to deselect it
Box Selection
- Click the Select button in the control bar
- Drag to draw a rectangle
- All proteins inside are selected
Additive Mode
When the Select button is active, all selections (clicks and box drags) are additive. Without it, each new selection replaces the previous one.
Clearing
- Press Escape to clear selections (first press), then exit selection mode (second press)
- Click the Clear button
Understanding the Display
Point Position
Points close together have similar embeddings - often indicating similar structure, function, or evolutionary history.
Point Colors
- Categorical (reviewed, protein family, species): Unique color per category
- Multi-label (EC numbers, domains): Pie charts showing multiple values
Protein Tooltip
Hover over a point to see a tooltip with details about that protein:
- Protein ID and UniProtKB ID (if available)
- Protein name and Gene name (if available)
- Annotation values for the currently selected annotation
- Scores (for InterPro domain annotations, e.g., E-values) or evidence codes (for GO terms, subcellular location, etc., e.g., EXP, IDA)
Protein name, gene name, and UniProtKB ID are tooltip-only and don't appear in the Annotation dropdown.
Duplicate Points
When multiple proteins share the exact same coordinates, a count badge appears on the point (when enabled in the legend settings). Click a stacked point to expand it into a spider layout showing each individual protein.