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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | RunTSNE(object, ...)
## S3 method for class 'matrix'
RunTSNE(object, assay = NULL, seed.use = 1,
tsne.method = "Rtsne", add.iter = 0, dim.embed = 2,
reduction.key = "tSNE_", ...)
## S3 method for class 'DimReduc'
RunTSNE(object, cells = NULL, dims = 1:5,
seed.use = 1, tsne.method = "Rtsne", add.iter = 0, dim.embed = 2,
reduction.key = "tSNE_", ...)
## S3 method for class 'Seurat'
RunTSNE(object, reduction = "pca", cells = NULL,
dims = 1:5, features = NULL, seed.use = 1, tsne.method = "Rtsne",
add.iter = 0, 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 |
tsne.method |
Select the method to use to compute the tSNE. Available methods are:
|
add.iter |
If an existing tSNE has already been computed, uses the current tSNE to seed the algorithm and then adds additional iterations on top of this |
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 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.