PaCMAP.Seurat: Pairwise Controlled Manifold Approximation (R wrapper)
In dbrookeUAB/dbsinglecell: Dewey Brooke's Single-Cell Toolkit

PaCMAP.Seurat

R Documentation

Pairwise Controlled Manifold Approximation (R wrapper)

Description

Pairwise Controlled Manifold Approximation (R wrapper)

Usage

## S3 method for class 'Seurat'
PaCMAP(
  object,
  reduction = "pca",
  reduction_name = "pacmap",
  dims = NULL,
  n_components = 2,
  n_neighbors = 10,
  MN_ratio = 0.5,
  FP_ratio = 2,
  num_iters = 450,
  pair_neighbors = NULL,
  pair_MN = NULL,
  pair_FP = NULL,
  lr = 1,
  apply_pca = TRUE,
  intermediate = FALSE,
  return_seurat = TRUE,
  nThreads = parallel::detectCores() - 1
)