`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:

Rtsne: Use the Rtsne package Barnes-Hut implementation of tSNE (default)

FIt-SNE: Use the FFT-accelerated Interpolation-based t-SNE. Based on Kluger Lab code found here: https://github.com/KlugerLab/FIt-SNE

- 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;

`dims`

must be NULL to run on features- 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