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 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 |
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.
Returns a MOFA
object with the MOFAobject@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 ## 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)