t-Distributed Stochastic Neighbor Embedding (t-SNE)

Perform t-SNE dimensionality reduction on the expression data. The function uses Rtsne::Rtsne() to perform t-SNE analysis.

Usage

gly_tsne(exp, dims = 2, perplexity = 30, add_info = TRUE, ...)

gly_tsne_(expr_mat, dims = 2, perplexity = 30, ...)

Arguments

exp: A glyexp::experiment() object containing expression matrix and sample information.
dims: Number of output dimensions. Default is 2.
perplexity: Perplexity parameter for t-SNE. Default is 30.
add_info: A logical value. If TRUE (default), sample information from the experiment will be added to the result tibble. If FALSE, only the t-SNE coordinates are returned. Only applicable to gly_tsne().
...: Additional arguments passed to Rtsne::Rtsne().
expr_mat: A numeric matrix with variables as rows and samples as columns.

Value

A list with two elements:

tidy_result: A tibble with t-SNE coordinates containing the following columns:
- sample: Sample name
- tsne1: First t-SNE dimension
- tsne2: Second t-SNE dimension
raw_result: The raw Rtsne object The list has classes glystats_tsne_res and glystats_res.

Details

gly_tsne() is the top-level API that works with glyexp::experiment() objects and supports the add_info parameter for joining experiment metadata.

gly_tsne_() is the underlying API that works with matrices directly, providing more flexibility for users who don't use the glyexp package.

Required packages