Subset

Core Feature

This feature is available in all MATISSE Explorer deployments.

The Subset feature allows you to build subset queries by combining multiple conditions with logical operators. This powerful tool enables precise data selection based on features, lasso selections, and signatures.

Opening the Subset Editor

Access the Subset Editor from the Explorer view:

1. Click the subset input field in the map viewer toolbar
2. The Subset Panel opens

Subset Structure

Subsets use a hierarchical structure:

Subset
├── Group 1
│   ├── Condition A  ─┬─ AND/OR
│   ├── Condition B  ─┤
│   └── Condition C  ─┘
│
├── AND/OR (group operator)
│
└── Group 2
    ├── Condition D  ─┬─ AND/OR
    └── Condition E  ─┘

• Conditions - Individual subset rules
• Groups - Collections of conditions combined with AND/OR
• Group Operator - Combines multiple groups with AND/OR

Condition Types

Column Condition

Select by feature values from your dataset.

For Categorical Columns:

• Select one or more categories to include
• Points matching any selected category pass the subset

For Continuous Columns:

• Set a value range or comparison
• Available operators:

  Operator	Meaning	Example
  Range	min ≤ value ≤ max	Expression between 0.5 and 2.0
  >	Greater than	Expression > 1.0
  ≥	Greater or equal	Expression ≥ 1.0
  <	Less than	Expression < 0.5
  ≤	Less or equal	Expression ≤ 0.5

Lasso Condition

Select by saved lasso selections.

Lasso conditions are created by:

1. Drawing a lasso selection on the map or scatter plot
2. Clicking "Add selection to subset"

Each lasso condition includes:

• Name - Descriptive name (auto-generated or custom)
• Source - Where it was drawn (Spatial, UMAP, t-SNE, or Scatter Plot)
• Polygon - The boundary coordinates (stored internally)

Signature Condition

Select by computed signature scores.

Configure:

• Signature - Select from your created signatures
• Combination Method - How to compute the score

  Method	Description
  Max	Maximum value across variables
  Min	Minimum value across variables
  Sum	Sum of all variable values
  Avg	Average of all variable values
  UMI Count	Normalized: ln(10000 × sum/totalUMI + 1)

• Comparison - Range or comparison operator with threshold

Creating Conditions

Add a New Condition

1. Click Add Condition within a group
2. Select the condition type (Column, Lasso, or Signature)
3. Configure the condition parameters
4. The subset updates preview automatically

Configure Column Condition

1. Click the column selector dropdown
2. Choose a feature column
3. For categorical: select categories from the list
4. For continuous: set operator and value(s)

Configure Lasso Condition

Lasso conditions are added from the map viewer:

1. Draw a lasso selection
2. Click "Add selection to subset" from the Items dropdown
3. The lasso appears as a condition in the subset editor

Configure Signature Condition

1. Select a signature from the dropdown
2. Choose the combination method
3. Set the comparison operator and value

Working with Groups

Add a New Group

1. Click Add Subset Group at the subset level
2. A new empty group appears
3. Add conditions to the group

Set Group Operator

Choose how conditions within a group combine:

• AND - All conditions must match (intersection)
• OR - Any condition can match (union)

Set Subset Group Operator

Choose how multiple groups combine:

• AND - Points must match all groups
• OR - Points can match any group

Logical Operators Explained

AND Logic

Condition A AND Condition B

Result: Only points that satisfy both conditions

Example: Cell type = "T cell" AND CD3E > 1.0 → Shows only T cells with high CD3E expression

OR Logic

Condition A OR Condition B

Result: Points that satisfy either or both conditions

Example: Cell type = "T cell" OR Cell type = "NK cell" → Shows all T cells and NK cells

Combining Groups

(A AND B) OR (C AND D)

Result: Points matching Group 1 OR points matching Group 2

Example:

• Group 1: Region A AND high expression
• Group 2: Region B AND low expression → Shows high expressors in Region A plus low expressors in Region B

Managing Conditions

Edit a Condition

Click on any condition parameter to modify it:

• Change the column/signature selection
• Adjust values or operators
• The subset recalculates automatically

Remove a Condition

1. Locate the condition to remove
2. Click the X or delete button
3. The condition is removed from the group

Remove a Group

1. Remove all conditions from the group, or
2. Click the group's delete button
3. The entire group is removed

Applying Subsets

Preview

As you build your subset, the map view updates to show matching points. The point count indicates how many items pass the subset.

Apply

Click Apply to confirm and apply the subset. The subset view becomes active.

Clear

Click Clear or remove all conditions to reset the subset and show all points.

Complex Subset Examples

Example 1: Specific Cell Type in Region

Goal: Find B cells in a specific tissue region

Group 1 (AND):
├── Column: cell_type = "B cell"
└── Lasso: "Germinal Center" (spatial selection)

Example 2: High Expression of Gene Set

Goal: Find cells highly expressing immune genes

Group 1 (AND):
├── Signature: "Immune Markers" (Max)
└── Comparison: > 2.0

Example 3: Multiple Regions Comparison

Goal: Compare two tissue regions

Subset (OR):
├── Group 1 (AND):
│   ├── Lasso: "Region A"
│   └── Column: n_genes > 1000
│
└── Group 2 (AND):
    ├── Lasso: "Region B"
    └── Column: n_genes > 1000

Tips and Best Practices

1. Start simple - Begin with one condition, then add complexity
2. Use preview - Check results as you build the subset
3. Name lasso selections - Use descriptive names for saved regions
4. Save subsets - Store frequently used subsets for reuse
5. Consider performance - Very complex subsets may take longer to compute

Troubleshooting

No Points Match

• Check if conditions are too restrictive
• Verify AND logic isn't excluding everything
• Try relaxing value ranges

Unexpected Results

• Review the logical operators (AND vs OR)
• Check group operator setting
• Verify column values are correct

Subset Not Updating

• Ensure changes are applied
• Check for loading indicators
• Refresh if necessary

Related Topics

• Lasso Selection - Creating lasso conditions
• Saved Subsets - Saving and loading subsets
• Signatures - Creating signatures