RunDiffusionMap: Run diffusion map

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Run diffusion map

Description

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.

Usage

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

## Not run: 
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')

## End(Not run)

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.