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