Control Bar Features

The control bar at the top provides tools for data management, selection, export, and import.

1. Projection Selector

Switch between different dimensionality reduction methods:

Method	Best For
PCA	Initial overview, finding outliers
UMAP	General exploration, balanced view
t-SNE	Finding clusters
PaCMAP	Fast alternative to t-SNE
MDS	Preserving distances

Different projections reveal different patterns - try switching between them!

3D Projections

When a 3D projection is available, a plane selector (XY / XZ / YZ) appears, letting you view different 2D slices of the 3D space.

2. Annotation Selector

Choose which annotation to use for coloring points:

The Annotation dropdown features:

• Grouped categories: Features are organized into sections (UniProt, InterPro, Taxonomy, Other)
• Search: Type to filter features by name (case-insensitive)
• Keyboard navigation: Use arrow keys to navigate, Enter to select, Escape to close

Only categories present in your dataset appear in the dropdown. Any columns that don't match a known category appear under Other. See the ProtSpace Python package for the complete list of available annotations per source.

Tooltip-only annotations

gene_name, protein_name, and uniprot_kb_id are excluded from the dropdown but are still shown in the tooltip on hover.

3. Search

Find specific proteins by ID:

1. Click inside the search box or press ⌘/Ctrl + K to focus it
2. Type a protein ID or partial match
3. Select from suggestions
4. Protein is selected in the scatterplot

Multiple IDs

Paste multiple IDs at once (newline or space separated) and all matching proteins will be selected. Useful for re-selecting a previously exported subset.

4. Select Button

Enable box selection mode to select multiple proteins at once. See the Box Selection section for details.

5. Clear Button

Click Clear (or press Escape) to remove all current selections. Pressing Escape again will exit selection mode.

6. Isolate Button

Isolate focuses on selected proteins by hiding all others:

1. Select one or more proteins (using search, click, or box select)
2. Click Isolate
3. Only selected proteins remain visible
4. Click Reset (appears when isolated) to restore all proteins

Use Case

Isolate is useful for examining relationships within a specific protein subset - hiding unrelated proteins reduces visual clutter.

7. Filter Button

Filter shows only proteins matching specific annotation criteria:

1. Click Filter to open the filter menu
2. Select one or more annotations to filter by (e.g., taxonomy, family)
3. Choose specific values for each annotation
4. Click Apply

Filtered proteins are highlighted with a custom color scheme.

Isolate vs Filter

• Isolate: Works with selected proteins - hides everything else
• Filter: Works with annotation values - highlights matches, dims non-matches

Use Isolate for ad-hoc selections (like search results). Use Filter for annotation-based queries (like "show all kinases").

8. Export

Click Export to save your visualization:

Format	Description
PNG	Raster image with legend
PDF	PDF document with legend
Protein IDs	Text file with newline-separated identifiers
Parquet	.parquetbundle file with all data and optional settings

See Exporting Results for image customization options (dimensions, legend size, font).

9. Import

Click Import to load a .parquetbundle file from your computer.

You can also drag & drop files directly onto the scatterplot.

Tips

• Compare projections: Patterns that appear in multiple projections are more reliable
• Use search: Quickly find known proteins to orient yourself
• Export often: Save interesting views for later

Next Steps

• Viewing 3D Structures - AlphaFold integration
• Exporting Results - Detailed export options