Package index

Main functions

The core functions to generate the 2D embeddings

tsne()

Rust-based t-SNE

umap()

Rust-based UMAP

phate()

Rust-based PHATE

kNN helpers

Everything and anything around kNN graph generation

generate_knn_graph()

Generate a k-nearest neighbour graph.

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

Synthetic data

manifold_synthetic_data()

Generate synthetic data for manifold learning

Params

Wrapper functions around core parameters

params_nn()

Wrapper function to generate nearest neighbour parameters

params_umap()

Wrapper function to generate UMAP parameters

params_tsne()

Wrapper function to generate t-SNE parameters

params_phate()

Wrapper function to generate PHATE parameters

Rust wrappers

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_data_clusters()

Generates clustered data

rs_data_swiss_role()

Generates the SwissRole data

rs_data_trajectory()

Generates tree-like data with branches

rs_phate()

Run PHATE dimensionality reduction

rs_phate_from_knn()

Run PHATE dimensionality reduction from a precomputed kNN graph

rs_tsne()

tSNE implementation

rs_tsne_from_knn()

tSNE implementation

rs_umap()

UMAP implementation

rs_umap_from_knn()

UMAP implementation

rs_check_cluster_separation()

Check cluster separation in an embedding