R/generics.R
, R/dimensional_reduction.R
RunTSNE.Rd
Run t-SNE 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 t-SNE call (most commonly used is perplexity) |
assay | Name of assay that that t-SNE is being run on |
seed.use | Random seed for the t-SNE. 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 |