Run diffusion map (DM)

Usage

RunDM(object, ...)

# S3 method for class 'Seurat'
RunDM(
  object,
  reduction = "pca",
  dims = 1:30,
  features = NULL,
  assay = NULL,
  layer = "data",
  ndcs = 2,
  sigma = "local",
  k = 30,
  dist.method = "euclidean",
  npcs = NULL,
  reduction.name = "dm",
  reduction.key = "DM_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

# Default S3 method
RunDM(
  object,
  assay = NULL,
  layer = "data",
  ndcs = 2,
  sigma = "local",
  k = 30,
  dist.method = "euclidean",
  npcs = NULL,
  reduction.key = "DM_",
  verbose = TRUE,
  seed.use = 11,
  ...
)

Arguments

object: An object. This can be a Seurat object or a matrix-like object.
...: Additional arguments to be passed to destiny::DiffusionMap.
reduction: Which dimensionality reduction to use. Default is "pca".
dims: The dimensions to be used. Default is NULL.
features: A character vector of features to use. Default is NULL.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
layer: Which layer to use. Default is data.
ndcs: A number of diffusion components (dimensions) to be computed. Default is 2.
sigma: The diffusion scale parameter of the Gaussian kernel. Currently supported values are "local" (default) and "global".
k: A number of nearest neighbors to be used for the construction of the graph. Default is 30.
dist.method: The distance metric to be used for the construction of the knn graph. Currently supported values are "euclidean" and "cosine". Default is "euclidean".
npcs: Number of principal components to use for dimensionality reduction before computing diffusion map. This can speed up computation when using many features. Default is NULL (auto-determined based on the number of features).
reduction.name: The name of the reduction to be stored in the Seurat object. Default is "dm".
reduction.key: The prefix for the column names of the basis vectors. Default is "DM_".
verbose: Whether to print the message. Default is TRUE.
seed.use: Random seed for reproducibility. Default is 11.