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Sample Drawer

Multi-Sample Session Specific

This feature is only available in multi-sample sessions.

The Sample Drawer is the side drawer dedicated to managing sample label groupings, configuring Group 1 vs. Group 2 statistical contrast pairs, and exploring comparative differential expression metrics across multi-sample cohorts.

Interface

The Sample Drawer is organized into three primary analysis tabs:

1. Sample Label Tab

The Sample Label Tab allows you to assign custom color tags and metadata groupings to samples:

Labeling Tools

  • Custom Sample Labels: Create custom label names (e.g. Control, Treated, WT, KO) and choose color palettes. Assign slides manually by clicking sample cards.
  • Automated Metadata Grouping ("Assign by Attribute"): Auto-generate labels and colors based on dataset metadata fields:
    • organism: Group slides by species (e.g. mouse, human).
    • tissue: Group slides by anatomical origin (e.g. brain, liver).
    • disease: Group slides by disease status (e.g. normal, Alzheimer).
    • platform: Group slides by technology platform (e.g. Seq-Scope, Visium HD).

2. Sample Compare Tab

The Sample Compare Tab configures statistical contrast pairs:

Contrast Setup

  • Group 1 vs. Group 2 Contrast: Assign labeled sample cohorts to Group 1 (Reference / Control) and Group 2 (Target / Treatment).
  • Statistical Method Selection:
    • Chi-Squared Test (chisq): Fast 2x2 contingency testing for transcript count and spatial proportion shifts.
    • DESeq2-inspired Model (deseq2): Real-time, in-browser Negative Binomial modeling with Median-of-Ratios size factor normalization for replicate-aware differential testing (see DESeq2-inspired Model).
  • Multiple Testing Corrections: Toggle Benjamini-Hochberg (BH FDR) or Šidák (FWER) adjustments.
  • Analysis Scopes: Choose between Gene Expression Comparison, Factor Weight Comparison, or Conditional Differential Expression (gene expression conditioned within a specific spatial factor domain).

3. Sample Stats Tab

The Sample Stats Tab presents interactive statistical analysis results:

Statistical Results

  • Interactive Volcano Plot: Plots fold-change (log2 FC) against statistical significance (-log10 FDR) with interactive tooltips and thresholds.
  • Statistical Data Tables: Browse complete results tables with fold-change, raw \(p\)-values, FDR, and FWER.
  • Data Export: Export statistical results tables in CSV, TSV, or JSON formats for downstream R / Python / Scanpy workflows.

Related Pages

Concepts

Manual Pages