Leiden Clustering

Overview

This block performs Leiden clustering on single-cell RNA-seq data using PCA embeddings as input. The input comes from upstream blocks such as Dimensionality Reduction. The output are identified cell clusters that can be visualized or used in downstream blocks (e.g., Cell Browser or Cluster Markers).

Pipeline context

This block typically follows dimensionality reduction and precedes cell type annotation and other downstream analyses.

 Blocks                                 Result pool
                                       ┌───────────
             ┌─────────────────────────┤
             │                         │
             v                         │
 ╔═══════════════════════════╗ exports │
 ║ Dimensionality Reduction  ║────->─-─┤ UMAP, t-SNE, PCA embeddings
 ╚═══════════════════════════╝         │ -----------------------------
                                       │
                                       ├ [sampleId][cellId] -> umap1, umap2, ...
             ┌─────────────────────────┤
             │                         │
             v                         │
 ╔═══════════════════════════╗ exports │
 ║     Leiden Clustering     ║────->─-─┤ Cluster assignments
 ╚═══════════════════════════╝         │ ---------------------
                                       │
                                       ├ [sampleId][cellId] -> clusterId
             ┌─────────────────────────┤
             │                         │
             v                         │
 ╔═══════════════════════╗             │
 ║  Downstream Analysis  ║             │
 ╚═══════════════════════╝             │

Core structure: axes and p-columns

The block consumes principal component analysis (PCA) embeddings and produces a p-column containing cluster assignments for each cell.

Primary axes

Axis Name	Type	Description
pl7.app/sampleId	String	Uniquely identifies the sample.
pl7.app/cellId	String	Uniquely identifies a single cell within a sample.

Input P-Columns

The block requires the principal component (PC) embeddings calculated by an upstream block like Dimensionality Reduction.

1. Principal Components

• P-column name: pl7.app/rna-seq/pcvalue
• Description: The principal component values for each cell, which are used to construct the k-nearest neighbor graph for clustering.
• Requirement: Required.
• Specification:

# --- Core Identity ---
name: pl7.app/rna-seq/pcvalue
valueType: Double

# --- Axes ---
axesSpec:
  - name: pl7.app/sampleId
    type: String
  - name: pl7.app/sc/cellId
    type: String
  - name: pl7.app/rna-seq/pc-num
    type: String

# --- Domain ---
domain:
  pl7.app/blockId: "..." # blockId from the upstream dimensionality reduction run
  pl7.app/rna-seq/batch-corrected": "false"

# --- Annotations ---
annotations:
  pl7.app/label: "Principal Component Value"

Exported P-Columns

The block exports a p-frame containing the new leidencluster p-column, which is intended for programmatic use by downstream blocks.

1. Leiden Cluster

• P-column name: pl7.app/rna-seq/leidencluster
• Description: The cluster assignment for each cell.
• Requirement: Required.
• Specification:

# --- Core Identity ---
name: pl7.app/rna-seq/leidencluster
valueType: String

# --- Axes ---
axesSpec:
  - name: pl7.app/sampleId
    type: String
  - name: pl7.app/cellId
    type: String

# --- Domain ---
domain:
  pl7.app/blockId: "..." # a unique identifier for the block run

# --- Annotations ---
annotations:
  pl7.app/label: "Cluster Resolution 1" # The resolution is a block parameter

Summary of Exported P-Columns

P-Column Name	Description	Axes	Requirement
pl7.app/rna-seq/leidencluster	The cluster assignment for each cell.	[sampleId][cellId]	Required