RunDiffusion: Run diffusion map

Description Usage Arguments Value

Description

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

Usage

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## 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.