run_tsne: Run t-SNE on the MOFA factors

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

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) 

bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.