Run Diffusion Map on a Seurat object

Run Diffusion Map on a Seurat object

RunDM(
  object,
  reduction = "pca",
  dims = 1:30,
  K = 10,
  sigma = NULL,
  n.components = 30,
  t = 1,
  dist.mat = NULL,
  reduction.key = "DM_"
)

Arguments

object

Seurat object

reduction

string; Dimensionality reduction to use, default: 'pca'

dims

integer; Which dimensions to use as input features

K

integer; Adaptive kernel bandwidth for each point set to be the distance to its K-th nearest neighbor.

sigma

numeric; Fixed kernel bandwidth, sigma will be ignored if K is specified.

n.components

integer; Number of leading nontrivial eigenvectors to export

t

integer; Number of diffusion times

dist.mat

matrix; Precomputed distance matrix (optional)

reduction.key

string; Dimensional reduction key, specifies the string before the number for the dimension names. 'DM_' by default

Value

Returns a Seurat object containing a Diffusion Map representation