Seurat (version 2.0.0)

RunDiffusion: Run diffusion map

Description

Run diffusion map

Usage

RunDiffusion(object, cells.use = NULL, dims.use = 1:5, genes.use = NULL,
  reduction.use = "pca", q.use = 0.01, max.dim = 2, scale.clip = 10,
  ...)

Arguments

object

Seurat object

cells.use

Which cells to analyze (default, all cells)

dims.use

Which dimensions to use as input features

genes.use

If set, run the diffusion map procedure on this subset of genes (instead of running on a set of reduced dimensions). Not set (NULL) by default

reduction.use

Which dimensional reduction (PCA or ICA) to use for the diffusion map. Default is PCA

q.use

Quantile to use

max.dim

Max dimension to keep from diffusion calculation

scale.clip

Max/min value for scaled data. Default is 3

...

Additional arguments to the diffuse call

Value

Returns a Seurat object with a diffusion map