Package index • manifoldsR

2D embedding methods

The core functions to generate the 2D embeddings

Everything and anything around kNN graph generation

generate_knn_graph(): Generate a k-nearest neighbour graph.
new_nearest_neighbour() generate_nearest_neigbours_class(): Generate a new NearestNeighbours
get_idx_mat(): Get the indices as a matrix
get_idx_flat(): Get the indices as a flat vector
get_dist_mat(): Get the indices as a matrix
get_dist_flat(): Get the distances as a flat vector

Various methods to do clustering in manifoldsR

best_membership(): Get the cluster membership at the best persistence score
calc_ari(): Adjusted Rand index calculation
calc_inertia(): Calculate the cluster inertia
calc_silhouette_score(): Calculates the Silhouette score of a given clustering
evoc(): Rust-based EVoC clustering
get_centroids(): Get cluster centroids
get_layer(): Get a specific EVoC layer
get_nearest_neighbours(): Get the kNN graph from an Evoc object
kmeans_cluster(): K-means clustering
membership(): Get cluster assignments

Wrapper functions around core parameters

params_clusters(): Parameters for clustered data generation
params_evoc(): Wrapper function to generate EVoC parameters
params_hierarchical(): Parameters for hierarchical cluster data generation
params_kmeans(): Wrapper function to generate k-means parameters
params_nn(): Wrapper function to generate nearest neighbour parameters
params_pacmap(): Wrapper function to generate PaCMAP parameters
params_diffusion_maps(): Wrapper function to generate diffusion maps parameters
params_phate(): Wrapper function to generate PHATE parameters
params_umap(): Wrapper function to generate UMAP parameters
params_swiss_role(): Parameters for swiss roll data generation
params_swiss_role_biased(): Parameters for swiss roll data generation
params_trajectory(): Parameters for trajectory data generation
params_tsne(): Wrapper function to generate t-SNE parameters

Everything rusty - only use this if you know what you are doing…

rs_approx_nearest_neighbours(): Wrapper around some nearest neighbour searches integrated into manifold-rs
rs_ari(): Adjusted Rand index
rs_check_cluster_separation(): Check cluster separation in an embedding
rs_data_biased_swiss_role(): Generates the SwissRole data
rs_data_clusters(): Generates clustered data
rs_data_swiss_role(): Generates the SwissRole data
rs_data_trajectory(): Generates tree-like data with branches
rs_data_hierarchical(): Generate hierarchical cluster data
rs_diffusion_maps(): Diffusion maps implementation
rs_diffusion_maps_from_knn(): Diffusion maps implementation with pre-computed kNN
rs_evoc(): EVoC clustering
rs_evoc_from_knn(): EVoC clustering from pre-computed kNN
rs_intertia(): Calculates the intertia for k-means clustering
rs_k_means(): Full k-means clustering
rs_k_means_mini_batch(): Mini-batch k-means clustering
rs_pacmap(): PaCMAP implementation
rs_pacmap_from_knn(): PaCMAP implementation with pre-computed kNN
rs_phate(): Run PHATE dimensionality reduction
rs_phate_from_knn(): Run PHATE dimensionality reduction from a precomputed kNN graph
rs_silhouette_score(): Calculates the cluster silhouette scores
rs_tsne(): tSNE implementation
rs_tsne_from_knn(): tSNE implementation
rs_umap(): UMAP implementation
rs_umap_from_knn(): UMAP implementation