compareEmb

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.

Provides functions for evaluating the stability of low-dimensional embeddings and cluster assignments in single‑cell RNA sequencing (scRNA‑seq) datasets. Starting from a principal component analysis (PCA) object, users can generate multiple replicates of t‑Distributed Stochastic Neighbor Embedding (t‑SNE) or Uniform Manifold Approximation and Projection (UMAP) embeddings. Embedding stability is quantified by computing pairwise Kendall’s Tau correlations across replicates and summarizing the distribution of correlation coefficients. In addition to dimensionality reduction, 'scStability' assesses clustering consistency using either Louvain or Leiden algorithms and calculating the Normalized Mutual Information (NMI) between all pairs of cluster assignments. For background on UMAP and t-SNE algorithms, see McInnes et al. (2020, <doi:10.21105/joss.00861>) and van der Maaten & Hinton (2008, <https://github.com/lvdmaaten/bhtsne>), respectively.

Ben Abrahams

scStability

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

compareEmb function

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

Arguments

Compare dimensional reduction embeddings and calculate stability statistics — compareEmb

<dl>

<dt>emb_list</dt>
<dd>A list of 2D embeddings (each typically containing coordinates for UMAP or t-SNE)
created by the <code>createEmb</code> function</dd>


<dt>n_cores</dt>
<dd>Integer specifying the number of CPU cores to use for parallelization (default: 1)</dd>


<dt>verbose</dt>
<dd>Whether the function should print summary statistics as it calculates them</dd>


<dt>print_plot</dt>
<dd>Whether the final violin plot should be automatically printed</dd>

</dl>

compareEmb: Compare dimensional reduction embeddings and calculate stability statistics

Description

Usage

Value

Arguments