Scatter Plot

Core Feature

This feature is available in all MATISSE Explorer deployments.

The Scatter Plot extension provides interactive two-dimensional visualizations for exploring relationships between annotations in your data. Configure custom axes, apply color mapping, and use lasso selection directly on plots.

Opening the Plot Extension

1. Click the Plot icon in the Activity Bar (left side)
2. The Sidebar shows plot configuration options
3. The Workspace displays the scatter plot

Configuring Axes

X Axis

Select what to display on the horizontal axis:

1. Click the X Axis selector
2. Choose from:
   • Continuous annotations (gene expression, metrics, embedding coordinates)
   • Variable Set scores
3. The plot updates with the new X axis

Y Axis

Select what to display on the vertical axis:

1. Click the Y Axis selector
2. Choose from the same options as X axis
3. The plot updates with the new Y axis

Variable Set Axes

When selecting a Variable Set for an axis:

1. Choose a Variable Set from the selector
2. Select a Method to combine variables:

Method	Description
Max	Maximum value among variables
Min	Minimum value among variables
Sum	Sum of variable values
Average	Average of variable values (default)
UMI Count	LogNorm: ln(10000 × sum/totalUMI + 1)

3. Configure the scale type as needed

Swap Axes

Click the Swap Axes button to exchange X and Y axis configurations, including their scale settings.

Common Axis Combinations

X Axis	Y Axis	Purpose
Gene A	Gene B	Compare expression of two genes
Gene	n_counts	Expression vs. sequencing depth
Variable Set A	Variable Set B	Compare pathway scores

Scale Types

For each axis, choose an appropriate scale:

Scale	Best For
Linear	Most data (default)
Log	Wide-ranging positive values
Log2	Wide-ranging positive values (base 2)
Log1p	Data with zeros, single-cell RNA-seq
SymLog	Data with negative values or zeros
Sqrt	Moderate compression
Power	Emphasize differences in small values

TIP

Log and Log2 scales are disabled when the minimum value is negative. Use SymLog or Log1p for data that includes zero or negative values.

Changing Scale

1. Locate the scale selector below each axis configuration
2. Select the desired scale type
3. The plot redraws with the new scaling

Color Mapping

Apply color to points based on annotation values:

Setting Color

1. Find the Color By selector in the sidebar
2. Choose an annotation:
   • Categorical: Points colored by category
   • Continuous: Points colored by value gradient
   • Variable Set: Points colored by computed score
3. The plot updates with colors

Continuous Color Settings

For continuous annotations and Variable Sets:

• Cutoff: Enable and adjust to filter out low values from the color scale (0-50%)
• Scale: Choose the scale type for color mapping
• Method (Variable Sets only): Select the combination method

Legend

The legend shows:

• Category names and colors (categorical)
• Color gradient with value range (continuous)

Plot Settings

Access plot settings through the Layers button (layer icon) in the top-right toolbar.

Feature Layer

Controls the opacity of all data points:

Control	Description
Opacity slider	0 (transparent) to 1 (opaque)
Eye toggle	Quick show/hide toggle

Point Size

Control	Description
Auto toggle	Enable automatic point sizing
Size slider	Manual size from 1px to 15px

Defaults:

• Auto: Enabled
• Size: 3px (when Auto is disabled)

Axis Title Size

Adjust the font size of axis titles (10-24px, default 14px).

Interacting with the Plot

Navigation

Action	Control
Pan	Click and drag
Zoom	Scroll wheel
Reset	Click the reset button (bottom-left)

TIP

Hold the Space key to temporarily switch to Pan mode while in Selection mode.

Hover Information

Hover over points to see:

• Point identifier (Spot ID)
• X axis column name and value
• Y axis column name and value
• Color annotation name and value
• Individual variable values (if coloring by Variable Set)

Lasso Selection on Scatter Plots

Select points directly on the scatter plot using lasso selection.

How to Select

1. Click the Selection button (Lasso icon) in the mode switcher at bottom center
2. Click and drag to draw a closed shape
3. Release to complete selection
4. Selected points are highlighted

Using Plot Selections

Selections made on scatter plots can be:

• Added to the Filter as lasso conditions
• Used to count specific populations
• Combined with other filter conditions

Selection Context

Lasso selections on scatter plots include:

• X axis column name
• Y axis column name
• X and Y scale types
• Polygon coordinates

This information is saved so the selection can be accurately reapplied.

Export

Export the scatter plot as an image:

1. Click the Export button (download icon) in the top-right toolbar
2. Click Capture PNG
3. The image is downloaded with axis labels and legend included

The exported image includes:

• All visible data points with current coloring
• Axis lines, labels, and titles
• Color legend (if color mapping is active)

Use Cases

Gene-Gene Comparison

Compare expression of two genes:

1. Set X = Gene A expression
2. Set Y = Gene B expression
3. Color by cell type
4. Identify co-expression patterns

Quality Control

Check data quality:

1. Set X = n_counts (total counts)
2. Set Y = n_genes (genes detected)
3. Color by a metric or cluster
4. Identify outliers or quality issues

Pathway Comparison

Compare variable set scores:

1. Create two Variable Sets
2. Set X = Variable Set A score
3. Set Y = Variable Set B score
4. Color by cell type
5. Find cells active in both pathways

Tips for Effective Plots

Choosing Axes

• Start with embeddings for overview
• Use gene pairs for co-expression analysis
• Try Variable Sets for pathway-level views

Optimizing Visibility

• Reduce point size for large datasets
• Lower feature layer opacity to see density
• Use log scale for expression data

Finding Patterns

• Try different color mappings
• Switch scales to reveal structure
• Use lasso to isolate clusters

Troubleshooting

Plot is Empty

• Check that X and Y axes are selected
• Verify data is loaded
• Check if filters are excluding all points

Points Overlap Too Much

• Reduce point size
• Lower feature layer opacity
• Try different scales

Colors Not Visible

• Check ColorBy selection
• Verify annotation has variation
• Adjust color range or cutoff

Slow Performance

• Large datasets may render slowly
• Try filtering to reduce point count
• Allow time for initial render

Related Topics

• Color Mapping - Color configuration details
• Variable Sets - Create axis variables
• Lasso Selection - Selection techniques
• Layer Settings - Point appearance settings