Volcano Plot

This function accepts a glyexp::experiment(), performs differential expression analysis using glystats::gly_limma(), and plots a volcano plot. There should be only two groups.

Usage

plot_volcano(exp, group_col = "group", p_adj_method = "BH", ref_group = NULL)

Arguments

exp

A glyexp::experiment() object.

group_col

A character string specifying the column name in sample information that contains group labels. Default is "group".

p_adj_method

A character string specifying the method to adjust p-values. See p.adjust.methods for available methods. Default is "BH". If NULL, no adjustment is performed.

ref_group

A character string specifying the reference group. If NULL (default), the first level of the group factor is used as the reference.

Value

A ggplot object.