Step: UMAP

Perform UMAP analysis using glystats::gly_umap() and plot a UMAP plot using glyvis::plot_umap(). Note that the result of UMAP largely depends on the n_neighbors 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_umap() with different n_neighbors 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_umap(
  on = "exp",
  n_neighbors = 15,
  n_components = 2,
  plot_width = 5,
  plot_height = 5,
  ...
)

Arguments

on: Name of the experiment to run UMAP 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".
n_neighbors: Number of neighbors to consider for each point. Default is 15.
n_components: Number of output dimensions. Default is 2.
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 uwot::umap().

Value

A glysmith_step object.

Details

Data required:

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

Data generated (with suffixes):

umap: The UMAP result

Plots generated (with suffixes):

umap: The UMAP plot

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step only when the user explicitly asks for UMAP.

Examples

step_umap()
#> <step "step_umap()"> UMAP
step_umap(n_neighbors = 15)
#> <step "step_umap(n_neighbors = 15)"> UMAP