sumapc: Sequential UMAP 2d embedding and simple 2d space partitioning...

In OuNao/sumapc: Sequential UMAP Clustering

Sequential UMAP 2d embedding and simple 2d space partitioning clustering.

Description

Sequential UMAP 2d embedding and simple 2d space partitioning clustering.

Usage

sumapc(
  data,
  maxevts = 10000L,
  transform_maxevts = 1000000L,
  maxlvl = 3L,
  minpts = 100L,
  clust_options = list(method = "sdbscan", mineps = 1, mindens = 0.1, bw = 0.05, nbins
    = 5, mvpratio = 0.5),
  multi_thread = TRUE,
  fast_sgd = TRUE,
  ret_model = FALSE,
  myqueue = NULL,
  verbose = FALSE,
  use_cuml = FALSE,
  seed = NULL,
  ...
)

Arguments

data	a data matrix.
maxevts	max number of random points to apply UMAP.
transform_maxevts	max number of points to apply UMAP transform. The points not used in the initial UMAP model are divided in batches of transform_maxevts points to apply UMAP transform. Lower value = lower memory usage.
maxlvl	max sequential levels to process.
minpts	min cluster size.
clust_options	list; 2d clustering options (see Details).
multi_thread	logical. Needs future package loaded and multisession plan selected to use parallel clustering (not only multithreading in UMAP). Only used if use_cuml = FALSE.
fast_sgd	logical; see umap.
ret_model	logical; should clustering model be exported.
myqueue	shinyQueue object. Multithreaded code use future package. This object is used to send log messages to the base worker. See shinyQueue.
verbose	logical.
use_cuml	logical. Enable CUML GPU compute acceleration.
seed	Integer or NULL.
...	additional parameters passed to UMAP

Details

clust_options must be a named list containing: method: one of "dbscan", "hdbscan", "kdbscan", "sdbscan" mineps: min eps value passed to dbscan mindens: min density passed to kdbscan bw: bw passed to sdbscan nbins: min number of bins of bw width mvpratio: max valley/peak ratio) Any other value is passed as is to the clustering method.

Value

A vector of cluster numbers with length = nrow(data)

OuNao/sumapc documentation built on May 5, 2024, 12:35 p.m.