R/generics.R
, R/dimensional_reduction.R
RunTSNE.Rd
Run tSNE dimensionality reduction on selected features. Has the option of running in a reduced dimensional space (i.e. spectral tSNE, recommended), or running based on a set of genes. For details about stored TSNE calculation parameters, see PrintTSNEParams
.
RunTSNE(object, ...) # S3 method for matrix RunTSNE( object, assay = NULL, seed.use = 1, tsne.method = "Rtsne", dim.embed = 2, reduction.key = "tSNE_", ... ) # S3 method for DimReduc RunTSNE( object, cells = NULL, dims = 1:5, seed.use = 1, tsne.method = "Rtsne", dim.embed = 2, reduction.key = "tSNE_", ... ) # S3 method for dist RunTSNE( object, assay = NULL, seed.use = 1, tsne.method = "Rtsne", dim.embed = 2, reduction.key = "tSNE_", ... ) # S3 method for Seurat RunTSNE( object, reduction = "pca", cells = NULL, dims = 1:5, features = NULL, seed.use = 1, tsne.method = "Rtsne", dim.embed = 2, distance.matrix = NULL, reduction.name = "tsne", reduction.key = "tSNE_", ... )
object  Seurat object 

...  Arguments passed to other methods and to tSNE call (most commonly used is perplexity) 
assay  Name of assay that that tSNE is being run on 
seed.use  Random seed for the tSNE. If NULL, does not set the seed 
tsne.method  Select the method to use to compute the tSNE. Available methods are:

dim.embed  The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE 
reduction.key  dimensional reduction key, specifies the string before the number for the dimension names. tSNE_ by default 
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 tSNE. Default is PCA 
features  If set, run the tSNE on this subset of features (instead of running on a set of reduced dimensions). Not set (NULL) by default; 
distance.matrix  If set, runs tSNE on the given distance matrix instead of data matrix (experimental) 
reduction.name  dimensional reduction name, specifies the position in the object$dr list. tsne by default 