RunTSNE | R Documentation |
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 class 'matrix'
RunTSNE(
object,
assay = NULL,
seed.use = 1,
tsne.method = "Rtsne",
dim.embed = 2,
reduction.key = "tSNE_",
...
)
## S3 method for class 'DimReduc'
RunTSNE(
object,
cells = NULL,
dims = 1:5,
seed.use = 1,
tsne.method = "Rtsne",
dim.embed = 2,
reduction.key = "tSNE_",
...
)
## S3 method for class 'dist'
RunTSNE(
object,
assay = NULL,
seed.use = 1,
tsne.method = "Rtsne",
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",
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. “ |
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.