Step: t-SNE

Perform t-SNE analysis using glystats::gly_tsne() and plot a t-SNE plot using glyvis::plot_tsne(). Note that the result of t-SNE largely depends on the perplexity parameter. Usually it's a trial-and-error process to find the best value iteratively. If you are not satisfied with the result, manually call glyvis::plot_tsne() with different perplexity values to find the best one.

This step depends on the on parameter (default: exp).

When on = "exp", requires exp (usually after step_preprocess()).
When on = "sig_exp", requires sig_exp from one of step_dea_limma(), step_dea_ttest(), step_dea_wilcox(), step_dea_anova(), or step_dea_kruskal().
When on = "trait_exp", requires trait_exp from step_derive_traits().
When on = "sig_trait_exp", requires sig_trait_exp from DEA on traits.
When on = "dynamic_motif_exp", requires dynamic_motif_exp from step_quantify_dynamic_motifs().
When on = "sig_dynamic_motif_exp", requires sig_dynamic_motif_exp from DEA on motifs.
When on = "branch_motif_exp", requires branch_motif_exp from step_quantify_branch_motifs().
When on = "sig_branch_motif_exp", requires sig_branch_motif_exp from DEA on motifs.

Usage

step_tsne(
  on = "exp",
  dims = 2,
  perplexity = 30,
  plot_width = 5,
  plot_height = 5,
  ...
)

Arguments

on: Name of the experiment to run t-SNE on. Can be "exp", "sig_exp", "trait_exp", "sig_trait_exp", "dynamic_motif_exp", "sig_dynamic_motif_exp", "branch_motif_exp", "sig_branch_motif_exp".
dims: Number of output dimensions. Default is 2.
perplexity: Perplexity parameter for t-SNE. Default is 30.
plot_width: Width of the plot in inches. Default is 5.
plot_height: Height of the plot in inches. Default is 5.
...: Additional arguments passed to Rtsne::Rtsne().

Value

A glysmith_step object.

Details

Data required:

exp (if on = "exp"): The experiment to perform t-SNE on
trait_exp (if on = "trait_exp"): The trait experiment to perform t-SNE on
dynamic_motif_exp (if on = "dynamic_motif_exp"): The dynamic motif experiment to perform t-SNE on
branch_motif_exp (if on = "branch_motif_exp"): The branch motif experiment to perform t-SNE on

Data generated (with suffixes):

tsne: The t-SNE result

Plots generated (with suffixes):

tsne: The t-SNE plot

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step only when the user explicitly asks for t-SNE.

Examples

step_tsne()
#> <step "step_tsne()"> t-SNE
step_tsne(perplexity = 30)
#> <step "step_tsne(perplexity = 30)"> t-SNE