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Run DM (diffusion map)

Source: R/RunDM.R
RunDM.Rd

Run DM (diffusion map)

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",
  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",
  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

The reduction to be used. Default is "pca".

dims

The dimensions to be used. Default is 1:30.

features

The features to be used. Default is NULL.

assay

The assay to be used. Default is NULL.

layer

The layer to be used. 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".

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

An integer specifying the random seed to be used. Default is 11.

Examples

pancreas_sub <- Seurat::FindVariableFeatures(pancreas_sub)
#> Finding variable features for layer counts
pancreas_sub <- RunDM(
  object = pancreas_sub,
  features = SeuratObject::VariableFeatures(pancreas_sub)
)
#> Warning: Layer ‘data’ is empty
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds
CellDimPlot(
  pancreas_sub,
  group.by = "CellType",
  reduction = "dm"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.