trajectory-inference

name	trajectory-inference
description	Infer cell trajectories using PAGA graph-based trajectory inference.
allowed-tools	Read, Bash
compatibility	scRNA-seq, snRNA-seq

Trajectory Inference

When to Use

To understand developmental trajectories and cell state transitions within a dataset.

Functions

paga_trajectory(adata, cluster_key="leiden", plot=True, output_dir=None) -> dict

Runs PAGA trajectory inference on AnnData.

Requires sc.pp.neighbors() and sc.tl.leiden() to have been run.

Returns dict with:

• connectivities_tree: PAGA tree as networkx graph
• plot_path: path to saved PAGA plot (if output_dir provided)

Parameters:

• cluster_key: Column in adata.obs for clustering
• plot: Whether to generate PAGA plot
• output_dir: Directory to save plot