RunSlingshot: Calculate Pseudotime and Map Trajectories Using Slingshot
In huayc09/SeuratExtend: SeuratExtend

RunSlingshot

R Documentation

Calculate Pseudotime and Map Trajectories Using Slingshot

Description

This function integrates Slingshot for pseudotime analysis directly within a Seurat workflow, enabling the mapping of cellular trajectories based on user-defined cluster assignments and starting clusters.

Usage

RunSlingshot(
  Seu,
  group.by,
  reducedDim = "PCA",
  assay = NULL,
  start.clus = NULL
)

Arguments

`Seu`	A Seurat object containing single-cell RNA-seq data with precomputed clusters and necessary dimensional reductions.
`group.by`	Specifies the metadata column in the Seurat object used to define groups or clusters for trajectory analysis.
`reducedDim`	The name of the dimensionality reduction to use for trajectory inference. Default: 'PCA'.
`assay`	Name of the assay to employ. Defaults to the active assay.
`start.clus`	Optional; specifies the starting cluster to initiate trajectory inference, which can be crucial for directing the trajectory analysis in a biologically meaningful way. Default: NULL.

Details

Slingshot is a flexible tool for trajectory analysis that uses cluster-based minimum spanning trees to infer developmental pathways. This function facilitates the integration of Slingshot with Seurat objects, allowing for pseudotime calculations that are sensitive to the underlying data structure and cluster dynamics. It is especially useful for complex datasets where multiple trajectories might exist, helping to uncover hidden patterns in cellular development.

Value

Modifies the Seurat object by adding Slingshot-derived pseudotime and trajectory data to the '@misc$slingshot' slot.

Examples

library(Seurat)
library(SeuratExtend)

# Load an example Seurat Object
mye_small <- readRDS(url("https://zenodo.org/records/10944066/files/pbmc10k_mye_small_velocyto.rds", "rb"))

# Run Slingshot
mye_small <- RunSlingshot(mye_small, group.by = "cluster", start.clus = "Mono CD14")

# Access and visualize the Slingshot output
sling <- mye_small@misc$slingshot$PCA$SlingPseudotime
print(head(sling))
mye_small@meta.data[,colnames(sling)] <- as.data.frame(sling)
DimPlot2(mye_small, features = colnames(sling), cols = "C")

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.