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Volcano plot of differentially expressed genes

Source: R/plot_volcano.R
plot_volcano.Rd

Volcano plot of differentially expressed genes

Usage

plot_volcano(
  top_table,
  x = "log2FC",
  y = "p_value_adj",
  fdr_cutoff = 0.05,
  max.overlaps = 30
)

Arguments

top_table

Data frame with columns that contain FC and P-values, default to log2FC and p_value_adj

x

Name of the column with logFC values

y

Name of the column with adjusted p-values

fdr_cutoff

Cutoff for labels to be plotted based on their adjusted p-values

max.overlaps

Maximum number of overlaps of points for package ggrepel

Value

ggpplot plot

Examples

data("mini_mac")
top_table <- mini_mac@tools$diff_exprs$Staurosporine_10
plot_volcano(top_table = top_table, max.overlaps = 100)
#> Warning: ggrepel: 353 unlabeled data points (too many overlaps). Consider increasing max.overlaps