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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 Factor

From top to bottom:

  • Collapse Button: Collapses the Explore Factor section.
  • Marker Gene Table: Indicates the action required to view a factor's marker gene table (e.g., "Single-Click" means single-clicking a factor chip reveals its table).
  • UMAP: Indicates the action required to highlight a factor in the UMAP plot (e.g., "Single-Click" highlights the factor).
  • Spatial Map: Indicates the action required to highlight a factor on the spatial map (e.g., "Double-Click" highlights the factor).

2. Factor Chips

2.1 Factor Control Bar

From left to right:

  • Export: Export files related to the factor layer. Click to view and select available files for download.
  • Alias: Click to open the Alias Dialog. You can rename factors manually or by uploading an alias file, or export the current aliases.
  • Colors: Click to open the Color Customization Dialog. You can manually assign colors or generate a random palette.
  • Mute/Unmute: Toggles the visibility of the factor layer.
  • Filter: Filters the factor table below based on ID, alias, weight, or top genes.
  • Search: Searches for specific factors within the table.

2.2 Factor Chip Grid

A grid of chips, each representing a distinct factor. Interact with a chip (single-click, double-click, or hover) to view details, see marker genes, or highlight the factor in the UMAP or spatial map, based on the Explore Factor configuration.

3.UMAP

3.1 UMAP controller

From left to right:

  • UMAP Settings: Click to adjust UMAP parameters, such as radius and dimming intensity (transparency of non-highlighted factors).
  • UMAP Window Size: Choose between "Small", "Medium", and "Large" display sizes for the UMAP plot.
  • Collapse Button: Collapses the UMAP section.

3.2 UMAP

An interactive UMAP plot where each point represents a spatial location or cell, colored by its dominant factor or cluster.

4. Factor Table

4.1 Factor Overview Table

By default, the factor table section shows the factor overview table, which shows the summary of all factors in this factor layer.

  • Sorting: Click column headers to sort the table.
  • Filtering/Search: Use the filter/search bar in the Factor Control Bar to refine the list.
  • Columns:
    • ID: Unique factor identifier.
    • Alias: Editable factor name.
    • Weight: Factor weight/abundance.
    • Top Genes: The top 5 genes defining the factor.

4.2 Single-Factor Marker Gene Table

When a factor chip is clicked, the factor table section shows the marker gene table of the factor.

Usage