run_tsne {MOFA2} | R Documentation

## Run t-SNE on the MOFA factors

### Description

Run t-SNE on the MOFA factors

### Usage

    run_tsne(object, factors = "all", groups = "all", ...)

### Arguments

`object` | a trained `MOFA` object.
`factors` | character vector with the factor names, or numeric vector with the indices of the factors to use, or "all" to plot all factors.
`groups` | character vector with the groups names, or numeric vector with the indices of the groups of samples to use, or "all" to use samples from all groups.
`...` | arguments passed to `Rtsne`

### Details

use set.seed before the function call to get reproducible results.

### Value

Returns a `MOFA` object with the dim_red slot filled with the t-SNE output

### Examples

    # Using an existing trained model on simulated data
    file <- system.file("extdata", "model.hdf5", package = "MOFA2")
    model <- load_model(file)

    # Run t-SNE
    ## Not run:  model <- run_tsne(model)

    # Change hyperparameters passed to Rtsne
    ## Not run:  model <- run_tsne(model, perplexity = 15)

[Package MOFA2 version 1.0.1 Index]