scStability: A user friendly wrapper function that runs the entire...

In scStability: Measuring the Stability of Dimension Reduction and Cluster Assignment in scRNA-Seq Experiments

A user friendly wrapper function that runs the entire scRNA-seq stability workflow and shows statistics for each step

Description

A wrapper function that runs all other stability analysis functions in order. Statistics for each step are printed accordingly and a final DR and cluster plot is shown which represents the medoid embeddings and cluster assignments that were generated.

Usage

scStability(
  seurat_obj,
  n_runs = 100,
  dr_method = "umap",
  clust_method = "louvain",
  n_cores = 1,
  verbose = TRUE,
  print_plot = TRUE,
  seeds = NULL
)

Arguments

seurat_obj	A Seurat object containing scRNA-seq data and a PCA
n_runs	Number of DR embeddings and number of cluster assignments to be generated (< 250 recommended)
dr_method	Method to use for dimension reduction, either "umap" or "tsne"
clust_method	Algorithm used for clustering, either "louvain" or "leiden"
n_cores	Number of CPU cores to use for parallelising functions
verbose	Whether the function should print summary statistics as it calculates them
print_plot	Whether the final medoid plot should be printed
seeds	A set of seeds of length n_runs used for generating embeddings and clusters

Value

A list containing:

mean_emb	Data frame containing the mean embedding coordinates
mean_clust	Vector of the mean cluster assignments
plot	ggplot2 object with the medoid embedding plot and cluster assignments
embedding_stats	List of embedding statistics
cluster_stats	List of clustering statistics
seurat_object	Seurat object now containing mean embeddings and mean clusters

scStability documentation built on June 23, 2025, 5:08 p.m.