Step: Volcano Plot — step_volcano • glysmith

Create a volcano plot from DEA results using glyvis::plot_volcano(). This step requires one of the DEA steps to be run:

step_dea_limma() (multi-group comparison is also supported)
step_dea_ttest()
step_dea_wilcox()

Usage

step_volcano(
  log2fc_cutoff = 1,
  p_cutoff = 0.05,
  p_col = "p_adj",
  plot_width = 5,
  plot_height = 6,
  ...
)

Arguments

log2fc_cutoff: The log2 fold change cutoff. Defaults to 1.
p_cutoff: The p-value cutoff. Defaults to 0.05.
p_col: The column name for p-value. Defaults to "p_adj". Can also be "p_val" (raw p-values without multiple testing correction).
plot_width: Width of the plot in inches. Default is 5.
plot_height: Height of the plot in inches. Default is 6.
...: Other arguments passed to EnhancedVolcano::EnhancedVolcano().

Value

A glysmith_step object.

Details

Data required:

dea_res: The DEA results from glystats::gly_limma()

Plots generated:

volcano: A volcano plot

AI Prompt

This section is for AI in inquire_blueprint() only.

Always include this step by default if DEA is performed, and the DEA method is not ANOVA or Kruskal-Wallis.

See also

glyvis::plot_volcano()

Examples

step_volcano()
#> <step "step_volcano()"> Volcano plot
step_volcano(log2fc_cutoff = 2)
#> <step "step_volcano(log2fc_cutoff = 2)"> Volcano plot