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.
...: Passed to destiny::DiffusionMap.
reduction: Linear reduction used as input.
dims: Dimensions to use. Supply only one of dims, features, neighbor, or graph.
features: Features used instead of a reduction.
assay: Assay to use. NULL uses the default assay.
layer: Assay layer to use.
ndcs: A number of diffusion components (dimensions) to be computed.
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.
dist.method: The distance metric to be used for the construction of the knn graph. Currently supported values are "euclidean" and "cosine".
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: Reduction to be stored in the Seurat object.
reduction.key: The prefix for the column names of the basis vectors.
verbose: Whether to print the message. Default is TRUE.
seed.use: Random seed.