RunDiffusionMap: Run Diffusion Map

Description

Run diffusion map dimensionality reduction on single-cell data.

Usage

RunDiffusionMap(object, ...)
# S3 method for default
RunDiffusionMap(
  object,
  assay = NULL,
  metric = "cosine",
  distance.matrix = NULL,
  ncomp = 20,
  reduction.name = "DiffMap",
  reduction.key = "DC_",
  weight.by.var = TRUE,
  verbose = TRUE,
  seed.use = 101,
  ...
)
# S3 method for Assay
RunDiffusionMap(
  object,
  assay = NULL,
  features = NULL,
  ncomp = 20,
  metric = "cosine",
  distance.matrix = NULL,
  reduction.name = "DiffMap",
  reduction.key = "DC_",
  weight.by.var = TRUE,
  verbose = TRUE,
  seed.use = 101,
  ...
)
# S3 method for StdAssay
RunDiffusionMap(
  object,
  assay = NULL,
  features = NULL,
  layer = "scale.data",
  ncomp = 20,
  metric = "cosine",
  distance.matrix = NULL,
  reduction.name = "DiffMap",
  reduction.key = "DC_",
  weight.by.var = TRUE,
  verbose = TRUE,
  seed.use = 101,
  ...
)
# S3 method for Seurat
RunDiffusionMap(
  object,
  assay = NULL,
  features = NULL,
  layer = "scale.data",
  ncomp = 20,
  metric = "cosine",
  distance.matrix = NULL,
  reduction.name = "DiffMap",
  reduction.key = "DC_",
  weight.by.var = TRUE,
  verbose = TRUE,
  seed.use = 101,
  ...
)

Value

Returns a DimReduc object with diffusion map results

Arguments

object: An object to run diffusion map on
...: Additional arguments to be passed to DiffusionMap()
assay: Name of Assay diffusion map is being run on
metric: This determines the choice of metric used to measure distance in the input space. Check DiffusionMap() for details. If a distance.matrix is provided, this will be ignored.
distance.matrix: If set, runs DiffusionMap on the given distance matrix instead of data matrix.
ncomp: Number of components to compute
reduction.name: the name of the DimReduc object
reduction.key: dimensional reduction key, specifies the string before the number for the dimension names.
weight.by.var: Weight the cell embeddings by the eigenvalues of the diffusion map
verbose: To print diagnostic messages. Default is TRUE.
seed.use: Set a random seed. Setting NULL will not set a seed.
features: Features to compute Diffusion Map
layer: The layer in assay to use when running diffusion map analysis.

Examples

Run this code

if (FALSE) {
# Run diffusion map on a Seurat object
seurat_obj <- RunDiffusionMap(seurat_obj, ncomp = 10)
}

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