Interactive Controls¶

Learn how to interact with SpatialVista visualizations in Jupyter.

3D/2D View Controls¶

Rotate: Drag or Shift + ↑↓←→
Pan: Shift + Drag or ↑↓←→
Zoom: Mouse wheel scroll

Annotation Panel¶

The left sidebar allows you to switch between different categorical annotations.

Features¶

Switch Annotations: Click on different annotation types to change the coloring
Hide/Show Categories: Click on category names in the legend to toggle visibility
Custom Colors: Click on color swatches to open the color picker and change category colors

Annotation Panel

Control Panel¶

The right panel provides controls for adjusting visualization parameters.

Control Panel

Point Size¶

Adjust the size of individual points in the visualization.

Use the slider to increase or decrease point size
Useful for sparse or dense datasets

Point Opacity¶

Control the transparency of points.

Lower values: More transparent (better for seeing overlapping structures)
Higher values: More opaque (better for sparse data)

Layout Modes¶

Switch between different spatial arrangements:

Original: Display points at their original coordinates
2D Treemap: Arrange points in a space-filling treemap layout
2D Histogram: Arrange points in histogram bins

Layout Modes

Continuous Values & Gene Expression¶

Selecting Variables¶

Use the dropdown menu to select continuous values or gene expression:

Continuous observations: QC metrics, cell scores, etc.
Gene expression: Any gene from your dataset

Threshold Slider¶

When a continuous value or gene is selected, a slider appears at the bottom:

Adjust threshold: Move the slider to filter points by value
Color gradient: The background shows the value range
Reset: Click the reset button to return to minimum value

Threshold Slider

View Switching¶

2D/3D Toggle¶

If your data has section information, you can switch between views:

3D View: Full 3D point cloud
2D View: Section-by-section 2D slices

Section Carousel¶

In 2D mode, use the section carousel to browse different slices:

Click thumbnails: Jump to a specific section
Preview: Each thumbnail shows a preview of that section

Section Carousel

Screenshots¶

Capture Current View¶

Click the camera icon in the header to save the current visualization:

Captures exactly what you see on screen
Downloads as PNG image
Includes current colors, filters, and layout

Next: Check the API Reference for programmatic control options.