RunDiffusion: Run diffusion map

In lyc-1995/MySeuratWrappers: My extentions to Seurat package

Description

Run a diffusion map dimensionality reduction. For details about stored difussion map calculation parameters, see PrintDiffusionParams.

Usage

## S3 method for class 'matrix'
RunDiffusion(
  object,
  assay = NULL,
  dim.embed = 2,
  q = 0.01,
  reduction.key = "DMC_",
  ...
)

## S3 method for class 'DimReduc'
RunDiffusion(
  object,
  cells = NULL,
  dims = 1:5,
  q = 0.01,
  dim.embed = 2,
  reduction.key = "DMC_",
  ...
)

## S3 method for class 'Seurat'
RunDiffusion(
  object,
  assay = NULL,
  cells = NULL,
  dims = 1:5,
  reduction = "diffusionmap",
  features = NULL,
  normalize.method = c("LogNormalize", "SCTransform"),
  q = 0.01,
  dim.embed = 2,
  scale.clip = 10,
  reduction.name = "diffusionmap",
  reduction.key = "DMC_",
  ...
)

RunDiffusion(object, ...)

Arguments

object	An object
assay	Name of Assay diffusion map is being run on
dim.embed	Total Number of diffusion map components (DMCs) to compute and store (2 by default)
q	Quantile to clip diffusion map components at. This addresses an issue where 1-2 cells will have extreme values that obscure all other points. 0.01 by default
reduction.key	dimensional reduction key, specifies the string before the number for the dimension names. DMC by default
...	Arguments passed to other methods and destiny
cells	Which cells to analyze (default, all cells)
dims	Which dimensions to use as input features.
reduction	Which dimensional reduction (e.g. PCA, ICA) to use for the diffusion map. Default is PCA
features	If set, run the diffusion map on this subset of features (instead of running on a set of reduced dimensions). Not set (NULL) by default; dims will automaticly be NULL to run on features
normalize.method	'LogNormalize' or 'SCTransform'. If NULL, set 'LogNormalize' by default
scale.clip	Max/min value for scaled data. Default is 10
reduction.name	dimensional reduction name, specifies the position in the object$dr list. diffusionmap by default

Value

Returns Seurat object with the diffusion map calculation stored in the reductions slot

lyc-1995/MySeuratWrappers documentation built on June 30, 2020, 11:48 a.m.