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Run PHATE on a SingleCells object

phate_sc.Rd

Wrapper around manifoldsR::phate() for the SingleCells class.

Usage

phate_sc(
  object,
  use_knn = TRUE,
  embd_to_use = "pca",
  no_embd_to_use = NULL,
  n_dim = 2L,
  k = 5L,
  knn_method = c("hnsw", "balltree", "annoy", "nndescent", "exhaustive"),
  nn_params = manifoldsR::params_nn(),
  phate_params = manifoldsR::params_phate(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

use_knn

Boolean. Use the kNN graph found in the object. Defaults to TRUE. If not available, will default to the embedding.

embd_to_use

String. The embedding to use for PHATE. Must be available in the object.

no_embd_to_use

Optional integer. Number of embedding dimensions to use. If NULL all will be used.

n_dim

Integer. Number of PHATE dimensions. Currently only 2L is supported. Defaults to 2L.

k

Integer. Number of nearest neighbours for graph construction. Defaults to 5L.

knn_method

String. Approximate nearest neighbour algorithm. One of "hnsw", "balltree", "annoy", "nndescent", or "exhaustive".

nn_params

Named list. See manifoldsR::params_nn().

phate_params

Named list. See manifoldsR::params_phate().

seed

Integer. For reproducibility.

.verbose

Boolean. Controls verbosity.

Value

The object with a "phate" embedding added.