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 use all factors (default).
`groups` | character vector with the groups names, or numeric vector with the indices of the groups of samples to use, or "all" to use all groups (default).
`...` | arguments passed to `Rtsne`

### Details

This function calls `Rtsne` to calculate a TSNE representation from the MOFA factors. Subsequently, you can plot the TSNE representation with `plot_dimred` or fetch the coordinates using `plot_dimred(..., method="TSNE", return_data=TRUE)`. Remember to use set.seed before the function call to get reproducible results.

### Value

Returns a `MOFA` object with the `MOFAobject@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
    ## Not run:  model <- run_tsne(model, perplexity = 15)

    # Plot
    ## Not run:  model <- plot_dimred(model, method="TSNE")

    # Fetch data
    ## Not run:  tsne.df <- plot_dimred(model, method="TSNE", return_data=TRUE)

[Package MOFA2 version 1.2.2 Index]