Step: Heatmap

Create a heatmap plot using glyvis::plot_heatmap(). The heatmap visualizes expression values across samples.

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_heatmap(on = "exp", plot_width = 7, plot_height = 7, ...)

Arguments

on: Name of the experiment data in ctx$data to plot. One of "exp", "sig_exp", "trait_exp", "sig_trait_exp", "dynamic_motif_exp", "sig_dynamic_motif_exp", "branch_motif_exp", "sig_branch_motif_exp". Default is "exp".
plot_width: Width of the plot in inches. Default is 7.
plot_height: Height of the plot in inches. Default is 7.
...: Additional arguments passed to glyvis::plot_heatmap().

Value

A glysmith_step object.

Details

Data required:

Depends on on parameter (default: exp)

Plots generated:

heatmap: A heatmap plot (if on = "exp")
sig_heatmap: A heatmap plot (if on = "sig_exp")
trait_heatmap: A heatmap plot (if on = "trait_exp")
sig_trait_heatmap: A heatmap plot (if on = "sig_trait_exp")
dynamic_motif_heatmap: A heatmap plot (if on = "dynamic_motif_exp")
sig_dynamic_motif_heatmap: A heatmap plot (if on = "sig_dynamic_motif_exp")
branch_motif_heatmap: A heatmap plot (if on = "branch_motif_exp")
sig_branch_motif_heatmap: A heatmap plot (if on = "sig_branch_motif_exp")

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step if needed.
It is recommended to use this step on significant results (e.g. on = "sig_exp") if available.

Examples