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t-Distributed Stochastic Neighbor Embedding (t-SNE)

gly_tsne.Rd

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, ...)

Arguments

exp

A glyexp::GlycomicSE() or glyexp::GlycoproteomicSE() object, or another SummarizedExperiment containing an 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.

...

Additional arguments passed to Rtsne::Rtsne().

Value

A list with three 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

  • meta_data: A list containing metadata from the input experiment The list has classes glystats_tsne_res and glystats_res.

Required packages

This function requires the Rtsne package to be installed for t-SNE analysis.

See also

Rtsne::Rtsne()