new_dim_reduction_config: Dimension Reduction Configuration Class

In topolow: Force-Directed Euclidean Embedding of Dissimilarity Data

Dimension Reduction Configuration Class

Description

S3 class for configuring dimension reduction parameters including method selection and algorithm-specific parameters.

Usage

new_dim_reduction_config(
  method = "pca",
  n_components = 2,
  scale = TRUE,
  center = TRUE,
  pca_params = list(tol = sqrt(.Machine$double.eps), rank. = NULL),
  umap_params = list(n_neighbors = 15, min_dist = 0.1, metric = "euclidean", n_epochs =
    200),
  tsne_params = list(perplexity = 30, mapping_max_iter = 1000, theta = 0.5),
  compute_loadings = FALSE,
  random_state = NULL
)

Arguments

method	Dimension reduction method ("pca", "umap", "tsne")
n_components	Number of components to compute
scale	Scale the data before reduction
center	Center the data before reduction
pca_params	List of PCA-specific parameters
umap_params	List of UMAP-specific parameters
tsne_params	List of t-SNE-specific parameters
compute_loadings	Compute and return loadings
random_state	Random seed for reproducibility

Value

An S3 object of class dim_reduction_config, which is a list containing the specified configuration parameters for dimensionality reduction.

topolow documentation built on Aug. 31, 2025, 1:07 a.m.