run_umap {MOFA2} | R Documentation

## Run UMAP on the MOFA factors

### Description

Run UMAP on the MOFA factors

### Usage

    run_umap(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 `umap`

### 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 UMAP output

### Examples

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

    # Run UMAP
    ## Not run:  model <- run_umap(model)

    # Change hyperparameters passed to umap
    ## Not run:  model <- run_umap(model, min_dist = 0.01, n_neighbors = 10)

[Package MOFA2 version 1.0.1 Index]