compareEmb: Compare dimensional reduction embeddings and calculate...

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

Compare dimensional reduction embeddings and calculate stability statistics

Description

Evaluates the stability of a set of dimension reduction embeddings by performing pairwise Procrustes alignment and calculating Kendall's Tau correlation between each pair. This function quantifies the consistency of embeddings generated with the same algorithm but different random initializations.

Usage

compareEmb(emb_list, n_cores = 1, verbose = TRUE, print_plot = TRUE)

Arguments

emb_list	A list of 2D embeddings (each typically containing coordinates for UMAP or t-SNE) created by the createEmb function
n_cores	Integer specifying the number of CPU cores to use for parallelization (default: 1)
verbose	Whether the function should print summary statistics as it calculates them
print_plot	Whether the final violin plot should be automatically printed

Value

A list containing the following components:

mean	Numeric value representing the overall mean correlation across all pairwise comparisons
mean_per_embedding	Numeric vector of mean correlation values for each embedding
all_pairwise_correlations	Numeric vector containing all pairwise correlation values
range	Numeric vector with minimum and maximum of mean correlation per embedding
ci	Numeric vector containing the lower and upper bounds of the 95% confidence interval

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