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!

URL persistence

Your current projection is reflected in the page URL, so refresh, browser back/forward navigation, and shared links reopen the same view when possible. A bare /explore URL stays unchanged on first load; ProtSpace writes projection and annotation params after you change the view or when it needs to normalize an invalid URL value.

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.

Shareable view state

The selected annotation is also stored in the page URL together with the current projection. This makes the current Explore view shareable and restorable across refreshes without reloading the page.

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. Selection Tools

Click Select to enter selection mode. A tool picker appears with two options:

• Rectangle (default) — drag to draw a box around proteins
• Lasso — draw a freeform outline around proteins

See Box Selection and Lasso Selection 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 opens a query builder modal for building complex annotation-based filters:

1. Click Filter to open the query builder
2. Each row is a condition: select an annotation, then click + to pick values
3. Combine conditions with AND, OR, or NOT logic
4. Use + Add group for nested logic (parenthetical grouping)
5. The live match count shows how many proteins match your query
6. Click Apply & Isolate to filter the scatterplot

Close the modal with the × button, Cancel, Escape key, or clicking the backdrop.

Reset All clears the query and restores all proteins without closing the modal.

Logical Operators

• AND: Protein must match both conditions
• OR: Protein must match either condition
• NOT: Protein must NOT match the condition (negation)

The first condition can optionally be set to NOT for immediate negation.

Filter vs Isolate

Both reduce visible proteins, but they work differently:

• Filter: Build annotation-based queries (e.g., "show all Human AND reviewed proteins")
• Isolate: Manually select proteins first, then hide everything else

Use Filter for structured queries. Use Isolate for ad-hoc selections.

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