Run diffusion map

This function is a wrapper to run the diffusion map dimensional reduction technique via package destiny. Details on this package can be found here: https://bioconductor.org/packages/release/bioc/html/destiny.html.

RunDiffusionMap(
  object,
  reduction.key = "DC_",
  assay = DefaultAssay(object = object),
  reduction = NULL,
  dims = NULL,
  k = NULL,
  seed = 42,
  verbose = TRUE,
  reduction.name = "dm"
)

Arguments

object

A Seurat object

reduction.key

dimensional reduction key, specifies the string before the number for the dimension names. DC by default

assay

Assay to pull data

reduction

Which dimensional reduction to use for the diffusion map input

dims

Which dimensions to use as input features

k

Number of nearest neighbors to consider. This is passed to the function DiffusionMap

seed

Random seed

verbose

Whether or not print running message

reduction.name

Name to store dimensional reduction under in the Seurat object. Default: dm

Value

Returns a Seurat object containing a diffusion map representation

Examples

if (FALSE) {
data("pbmc_small")
# Run diffusion map on first 5 PCs
pbmc_small <- RunDiffusionMap(object = pbmc_small, reduction = "pca",
dims = 1:20, k = 10)
# Plot results
DimPlot(object = pbmc_small, reduction = 'dm')
}