createEmb: Create multiple dimension reduction embeddings

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

Create multiple dimension reduction embeddings

Description

Generates multiple dimension reduction embeddings using either UMAP or t-SNE algorithms. Each embedding is created with different random initializations to assess stability. The function returns a list of embeddings, each represented as a data frame or matrix.

Usage

createEmb(
  dr_input,
  n_runs = 100,
  method = c("umap", "tsne"),
  n_neighbors = 15,
  min_dist = 0.1,
  perplexity = 30,
  theta = 0.5,
  n_cores = 1,
  seeds = NULL
)

Arguments

dr_input	A numeric matrix or data frame containing the input data for dimension reduction, with rows representing observations (cells) and columns representing PCA components
n_runs	Integer specifying the number of embeddings to generate (default: 100)
method	Character string specifying the dimension reduction method to use: either "umap" or "tsne"
n_neighbors	Integer specifying the number of neighbors to consider when constructing the initial graph (used for UMAP only, default: 30)
min_dist	Numeric value specifying the minimum distance between points in the embedding (used for UMAP only, default: 0.1)
perplexity	Numeric value controlling the effective number of neighbors (used for t-SNE only, default: 30)
theta	Numeric value between 0 and 1 controlling the speed/accuracy trade-off (used for t-SNE only, default: 0.5)
n_cores	Integer specifying the number of CPU cores to use for parallelization (default: 1)
seeds	A set of seeds of length n_runs to be used for each embedding

Value

A list of dimension reduction embeddings, each represented as a data frame with rows corresponding to observations (cells) and two columns representing the x and y coordinates in the reduced space.

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