Step: Significant Variables Boxplot

Create boxplots for the most significant variables from DEA analysis using glyvis::plot_boxplot(). The function selects the top n_top variables with the lowest adjusted p-values from the DEA results and plots their expression values grouped by sample groups.

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

• 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 = "sig_trait_exp", requires sig_trait_exp from DEA on traits.

• When on = "sig_dynamic_motif_exp", requires sig_dynamic_motif_exp from DEA on motifs.

• When on = "sig_branch_motif_exp", requires sig_branch_motif_exp from DEA on motifs.

The number of variables is limited to a maximum of 25, as enforced by glyvis::plot_boxplot().

Usage

step_sig_boxplot(
  on = "sig_exp",
  n_top = 25,
  panel_width = 1.5,
  panel_height = 1.2,
  min_width = 5,
  min_height = 3,
  max_width = 14,
  max_height = 12,
  ...
)

Arguments

on

Name of the experiment data in ctx$data to plot. One of "sig_exp", "sig_trait_exp", "sig_dynamic_motif_exp", "sig_branch_motif_exp". Default is "sig_exp".

n_top

Number of top significant variables to plot. Must be between 1 and 25 (inclusive). Default is 25.

panel_width

Width of each panel in inches. Default is 1.5.

panel_height

Height of each panel in inches. Default is 1.2.

min_width

Minimum plot width in inches. Default is 5.

min_height

Minimum plot height in inches. Default is 3.

max_width

Maximum plot width in inches. Default is 14.

max_height

Maximum plot height in inches. Default is 12.

...

Additional arguments passed to glyvis::plot_boxplot().

Value

A glysmith_step object.

Details

Data required:

• Depends on on parameter:

  • sig_exp (default): Significant experiment from DEA

  • sig_trait_exp: Significant trait experiment from DTA

  • sig_dynamic_motif_exp: Significant dynamic motif experiment from DMA

  • sig_branch_motif_exp: Significant branch motif experiment from DMA

Plots generated:

• sig_boxplot: A boxplot of significant variables (if on = "sig_exp")

• sig_trait_boxplot: A boxplot of significant traits (if on = "sig_trait_exp")

• sig_dynamic_motif_boxplot: A boxplot of significant dynamic motifs (if on = "sig_dynamic_motif_exp")

• sig_branch_motif_boxplot: A boxplot of significant branch motifs (if on = "sig_branch_motif_exp")

See also

glyvis::plot_boxplot()

Examples

step_sig_boxplot()
#> <step "step_sig_boxplot()"> Significant variables boxplot of significant
#> variables
step_sig_boxplot(n_top = 12)
#> <step "step_sig_boxplot(n_top = 12)"> Significant variables boxplot of
#> significant variables
step_sig_boxplot(on = "sig_trait_exp")
#> <step "step_sig_boxplot(on = \"sig_trait_exp\")"> Significant variables boxplot
#> of significant traits