Package: manifoldsR 0.5.0

manifoldsR: Fast Low-Dimensional Embeddings and Clustering via 'Rust'

R interface to the Rust crates 'manifolds-rs', 'ann-search-rs' and 'evoc-rs'. Builds 2D (or higher) embeddings with UMAP (McInnes et al., 2018) <doi:10.48550/arXiv.1802.03426>, t-SNE (van der Maaten and Hinton, 2008) <https://jmlr.org/papers/v9/vandermaaten08a.html>, densMAP and den-SNE (Narayan et al., 2021) <doi:10.1038/s41587-020-00801-7>, PHATE (Moon et al., 2019) <doi:10.1038/s41587-019-0336-3>, PaCMAP (Wang et al., 2021) <https://jmlr.org/papers/v22/20-1061.html>, ForceAtlas2 (Jacomy et al., 2014) <doi:10.1371/journal.pone.0098679>, DREAMS and diffusion maps. Also generates approximate nearest neighbour graphs that every method can reuse, plus EVoC and k-means clustering. Multi-threaded via 'Rayon', with f32 or f64 precision.

Authors:Gregor Lueg [aut, cre], Grant Neilson [aut], Authors of the dependency Rust crates [ctb, cph]

manifoldsR_0.5.0.tar.gz
manifoldsR_0.5.0.zip(r-4.7-x86_64)manifoldsR_0.5.0.zip(r-4.7-arm64)manifoldsR_0.5.0.zip(r-4.6-x86_64)manifoldsR_0.5.0.zip(r-4.6-arm64)manifoldsR_0.5.0.zip(r-4.5-x86_64)
manifoldsR_0.5.0.tgz(r-4.6-x86_64)manifoldsR_0.5.0.tgz(r-4.6-arm64)manifoldsR_0.5.0.tgz(r-4.5-x86_64)manifoldsR_0.5.0.tgz(r-4.5-arm64)
manifoldsR_0.5.0.tar.gz(r-4.7-arm64)manifoldsR_0.5.0.tar.gz(r-4.7-x86_64)manifoldsR_0.5.0.tar.gz(r-4.6-arm64)manifoldsR_0.5.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
manifoldsR/json (API)

# Install 'manifoldsR' in R:
install.packages('manifoldsR', repos = c('https://gregorlueg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gregorlueg/manifoldsr/issues

Pkgdown/docs site:https://gregorlueg.github.io

On CRAN:

Conda:

phaterustsingle-celltsneumapcargo

4.26 score 2 stars 3 packages 92 exports 9 dependencies

Last updated from:0f6a3365eb (on v0.5.0). Checks:14 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK274
linux-devel-x86_64OK336
source / vignettesOK443
linux-release-arm64OK290
linux-release-x86_64OK336
macos-release-arm64OK467
macos-release-x86_64OK884
macos-oldrel-arm64OK544
macos-oldrel-x86_64OK656
windows-devel-arm64OK548
windows-devel-x86_64OK577
windows-release-arm64OK505
windows-release-x86_64OK386
windows-oldrel-x86_64OK554
wasm-releaseFAIL123

Exports:.prepare_densmap_params.prepare_densne_params.prepare_diffusion_maps_params.prepare_dreams_params.prepare_evoc_params.prepare_fa2_params.prepare_pacmap_params.prepare_tsne_params.prepare_umap_paramsbest_membershipcalc_aricalc_inertiacalc_silhouette_scoredensmapdensnediffusion_mapsdreamsevocforceatlas2forceatlas2_from_graphgenerate_knn_graphgenerate_nearest_neigbours_classget_centroidsget_dist_flatget_dist_matget_idx_flatget_idx_matget_layerget_nearest_neighbourskmeans_clustermanifold_synthetic_datamembershipnew_nearest_neighbourpacmapparams_clustersparams_densmapparams_densneparams_diffusion_mapsparams_dreamsparams_evocparams_fa2params_hierarchicalparams_kmeansparams_nnparams_pacmapparams_phateparams_swiss_roleparams_swiss_role_biasedparams_swiss_rollparams_swiss_roll_biasedparams_trajectoryparams_tsneparams_umapphaters_approx_nearest_neighboursrs_arirs_check_cluster_separationrs_data_biased_swiss_rolers_data_biased_swiss_rollrs_data_clustersrs_data_hierarchicalrs_data_swiss_rolers_data_swiss_rollrs_data_trajectoryrs_densmaprs_densmap_from_knnrs_densners_densne_from_knnrs_diffusion_mapsrs_diffusion_maps_from_knnrs_dreamsrs_dreams_from_knnrs_evocrs_evoc_from_knnrs_forceatlas2rs_forceatlas2_from_graphrs_forceatlas2_from_knnrs_inertiars_intertiars_k_meansrs_k_means_mini_batchrs_pacmaprs_pacmap_from_knnrs_phaters_phate_from_knnrs_silhouette_scorers_tsners_tsne_from_knnrs_umaprs_umap_from_knntsneumap

Dependencies:backportscheckmatecligluelifecyclemagrittrpurrrrlangvctrs

Readme and manuals

Help Manual

Help pageTopics
Get the cluster membership at the best persistence scorebest_membership best_membership.Evoc
Adjusted Rand index calculationcalc_ari
Calculate the cluster inertiacalc_inertia calc_inertia.KMeansCluster
Calculates the Silhouette score of a given clusteringcalc_silhouette_score
Rust-based densMAPdensmap
Rust-based den-SNEdensne
Rust-based diffusion mapsdiffusion_maps
Rust-based DREAMSdreams
Rust-based EVoC clusteringevoc
Rust-based ForceAtlas2forceatlas2
Rust-based ForceAtlas2 on a pre-computed graphforceatlas2_from_graph
Generate a k-nearest neighbour graph.generate_knn_graph
Get cluster centroidsget_centroids get_centroids.KMeansCluster
Get the distances as a flat vectorget_dist_flat get_dist_flat.NearestNeighbours
Get the indices as a matrixget_dist_mat get_dist_mat.NearestNeighbours
Get the indices as a flat vectorget_idx_flat get_idx_flat.NearestNeighbours
Get the indices as a matrixget_idx_mat get_idx_mat.NearestNeighbours
Get a specific EVoC layerget_layer get_layer.Evoc
Get the kNN graph from an Evoc objectget_nearest_neighbours get_nearest_neighbours.Evoc
K-means clusteringkmeans_cluster
Generate synthetic data for manifold learningmanifold_synthetic_data
Get cluster assignmentsmembership membership.KMeansCluster
Generate a new NearestNeighboursgenerate_nearest_neigbours_class new_nearest_neighbour
Rust-based PaCMAPpacmap
Parameters for clustered data generationparams_clusters
Wrapper function to generate densMAP parametersparams_densmap
Wrapper function to generate den-SNE parametersparams_densne
Wrapper function to generate diffusion maps parametersparams_diffusion_maps
Wrapper function to generate DREAMS parametersparams_dreams
Wrapper function to generate EVoC parametersparams_evoc
Wrapper function to generate ForceAtlas2 parametersparams_fa2
Parameters for hierarchical cluster data generationparams_hierarchical
Wrapper function to generate k-means parametersparams_kmeans
Wrapper function to generate nearest neighbour parametersparams_nn
Wrapper function to generate PaCMAP parametersparams_pacmap
Wrapper function to generate PHATE parametersparams_phate
Parameters for swiss roll data generationparams_swiss_roll
Parameters for biased swiss roll data generationparams_swiss_roll_biased
Parameters for trajectory data generationparams_trajectory
Wrapper function to generate t-SNE parametersparams_tsne
Wrapper function to generate UMAP parametersparams_umap
Rust-based PHATEphate
Wrapper around some nearest neighbour searches integrated into manifold-rsrs_approx_nearest_neighbours
Adjusted Rand indexrs_ari
Generates biased Swiss roll datars_data_biased_swiss_roll
Generates clustered datars_data_clusters
Generate hierarchical cluster datars_data_hierarchical
Generates Swiss roll datars_data_swiss_roll
Generates tree-like data with branchesrs_data_trajectory
densMAP implementationrs_densmap
densMAP implementationrs_densmap_from_knn
den-SNE implementationrs_densne
den-SNE implementationrs_densne_from_knn
Diffusion maps implementationrs_diffusion_maps
Diffusion maps implementation with pre-computed kNNrs_diffusion_maps_from_knn
DREAMS implementationrs_dreams
DREAMS implementationrs_dreams_from_knn
EVoC clusteringrs_evoc
EVoC clustering from pre-computed kNNrs_evoc_from_knn
ForceAtlas2 implementationrs_forceatlas2
ForceAtlas2 on a pre-computed graphrs_forceatlas2_from_graph
ForceAtlas2 implementationrs_forceatlas2_from_knn
Calculates the inertia for k-means clusteringrs_inertia
K-means clustering (full)rs_k_means
Mini-batch k-means clusteringrs_k_means_mini_batch
PaCMAP implementationrs_pacmap
PaCMAP implementation with pre-computed kNNrs_pacmap_from_knn
Run PHATE dimensionality reductionrs_phate
Run PHATE dimensionality reduction from a precomputed kNN graphrs_phate_from_knn
Calculates the cluster silhouette scoresrs_silhouette_score
tSNE implementationrs_tsne
tSNE implementationrs_tsne_from_knn
UMAP implementationrs_umap
UMAP implementationrs_umap_from_knn
Rust-based t-SNEtsne
Rust-based UMAPumap