Quick Start Guide

Core Feature

This feature is available in all Portrai Explorer deployments.

Get started with Portrai Explorer in just a few minutes. This guide walks you through the essential steps to explore your spatial transcriptomics data.

Step 1: Open Your Project

InSilicoLab Users

If you are using InSilicoLab, select your project from the Reports section to open Portrai Explorer.

When you launch Portrai Explorer, your project data loads automatically. You will see:

• The map viewer displaying your tissue image with data points
• The Sidebar showing available features
• Loading indicators while data is being fetched

Wait for the data to finish loading before proceeding. Large datasets may take a moment to fully render.

Step 2: Color by Feature

Apply color mapping to visualize patterns in your data:

1. In the Sidebar, browse the Features list
2. Click the Metadata tab to see observation-level features such as cell types
3. Click on a feature name (e.g., "cell_type") to select it
4. The map updates to show data points colored by the selected feature

Try Different Feature Types

• Categorical - Discrete categories like cell types or clusters
• Continuous - Numeric values like gene expression levels
• Signatures - Combined scores of several variables, listed in the Signatures tab

Embeddings such as UMAP are not colorable features. They are map projections, selected with the projection selector in the toolbar.

Step 3: Navigate the Map

Explore your data using mouse controls:

Action	Control
Pan	Click and drag
Zoom in	Scroll wheel up or double-click
Zoom out	Scroll wheel down
Reset view	Click Reset View, the crosshair button in the bottom-left corner of the map

Step 4: Apply a Subset

Narrow down your data to specific populations:

1. Click the subset input field in the toolbar to open the Subset Panel
2. Click Add Condition to create a new subset rule
3. Select a feature and set your criteria
4. The subset applies automatically (Auto apply is enabled by default)

Only data points matching your subset criteria will remain visible. The point count updates to show how many points pass the subset.

Step 5: Select a Region

Select specific regions interactively:

1. Click the Lasso button in the mode switcher at the bottom of the map, or press S
2. Draw a closed shape around your region of interest
3. Release to complete the selection
4. View the count of selected points

For a region that is easier to paint than to outline in one go, use the Brush (B) instead and build it up stroke by stroke. See Brush Selection.

What You Can Do With Selections

• Add the selection as a subset condition
• View statistics for selected points
• Export selected data

Step 6: Add a Plot

The Plot extension is a multi-plot dashboard that can hold several plots at once. To add your first plot:

1. Click the Plot icon in the Activity Bar
2. Click New Plot in the Sidebar and choose a type from the catalog (Scatter Plot, Bar Plot, Stacked Bar Plot, Violin Plot, Dot Plot, or Box Plot)
3. A panel is added to the dashboard and becomes the active plot
4. Use the Settings panel in the Sidebar to configure the active plot - for example, set the X and Y axes and an optional color mapping for a Scatter Plot

You can add more plots and arrange them in the grid. See Plot Dashboard for the full tour.

Next Steps

Now that you know the basics, explore more features:

• Map Viewer - Detailed map viewer documentation
• Subset - Build complex subset queries
• Signatures - Create custom gene groups
• Tutorials - Step-by-step workflow guides

Tips for New Users

1. Start with categorical features - They provide clear visual groupings
2. Use the Detail Panel - Its category colors or histogram show the color mapping; hover a category or a histogram bar to show only those points on the map
3. Save subsets - Reuse complex subset configurations
4. Try different projections - Switch between spatial, UMAP, and t-SNE views
5. Export early, export often - Save subset data for downstream analysis