RunDiffusion: Run diffusion map
In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Run diffusion map

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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,
  reduction.name = "dm", reduction.key = "DM", ...)

`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
`reduction.name`	dimensional reduction name, specifies the position in the object$dr list. dm by default
`reduction.key`	dimensional reduction key, specifies the string before the number for the dimension names. DM by default
`...`	Additional arguments to the diffuse call