run_tsne {MOFA2} | R Documentation |
Run t-SNE on the MOFA factors
run_tsne(object, factors = "all", groups = "all", ...)
object |
a trained |
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 |
use set.seed before the function call to get reproducible results.
Returns a MOFA
object with the dim_red slot filled with the t-SNE output
# 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)