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Factor Drawer

The Factor Drawer is designed for exploring spatial factors, cell types, and other high-level biological features inferred from your data.

Functionality

Display the details of one factor set layer, and support to manage and explore the factor set layer. It currently allows the following operations:

  • Display Factor Details: View color, alias, weight, and top genes for all factors; visualize relationships using UMAP; and inspect marker genes for individual factors.
  • Interaction: Interact with the UMAP and main spatial map to highlight specific factors (see "Explore Factor" section).
  • Export and Management: Upload or export relevant factor layer files; customize factor colors and aliases.

Interface

Factor Drawer

1. Factor Overview Controller

1.1 Factor Name

Displays the name of the active factor layer. Click to open the dropdown menu to switch between available factor layers.

1.2 Explore Factors

A collapsible summary of the factor set's capabilities:

  • Collapse Button: Collapses the Explore Factor section.
  • Analysis: (If applicable) Indicates analysis type, e.g., "Multi-sample FICTURE".
  • Marker Gene Table: Indicates availability.
  • UMAP: Indicates availability and interaction trigger (e.g., "Hover" or "Double-Click").
  • Spatial Map: Indicates availability. If interactive, allows toggling between Double-Click (pin) and Hover (preview) modes.

2. Factor Chips

2.1 Factor Control Bar

From left to right:

  • Export: Download related files (DE, Pseudobulk, Model, Summary, UMAP data/images).
  • Colors: Open the Color Customization panel to assign colors manually or shuffle them.
  • Reset: Resets all factor visibility and selections to default.
  • View: Configures how unselected factors appear on the spatial map (Original colors with opacity vs. Single color).
  • Collapse/Expand Icon: Toggles the visibility of the factor chip list.

2.2 Factor Chip Grid

A color-coded grid of chips representing each factor.

  • Interaction: Click a chip to view its details in the bottom panel.

  • Visibility: Toggle checkboxes to show/hide specific factors on the map (if supported).

    Factor Summary

    Hovering over a factor chip will display a summary card of the factor, including its alias, weight, and top genes. Factor Summary

3. UMAP

An interactive UMAP plot (if available) showing the relationships between factors or samples.

4. Factor Details / Bottom Panel

4.1 Factor Overview Table (Default)

By default, the bottom panel displays a summary table of all factors:

  • Columns: ID, Alias (editable), Weight, Top Genes.
  • Actions: Sort by columns, or click the "Edit Alias" icon to rename factors.

4.2 Single-Factor View

When a factor chip is clicked, a detailed view for that factor appears:

  • Header: Displays the Factor Name and navigation controls.
  • Tabs:
    • Genes: A table of marker genes for the selected factor. Includes a toolbar for Filter and Search.
    • Volcano: A volcano plot visualizing differential expression (if supported).
  • Gene Group Controls: Options to add selected marker genes as a new layer or group.

Usage

For step-by-step instructions, please refer to:

FAQ