Skip to contents

Plot (DE genes) volcano plot

Source: R/DEgenes.R
plot_volcano.Rd

Wrapper for EnhancedVolcano::EnhancedVolcano() with additional caption and saving

Usage

plot_volcano(
  df,
  names = "gene",
  x = "log2FoldChange",
  y = "pvalue",
  pCutoff = 5e-04,
  FCcutoff = 1,
  xlab_high = NULL,
  xlab_low = NULL,
  xlab_size = 7,
  title = NULL,
  subtitle = NULL,
  savename = NULL,
  height = 12,
  width = 16
)

Arguments

df

df/string; (path to) test statistics, w/ cols names, x, y

names

string; colname in df w/ feature names (genes)

x

string; colname for log2 fold changes

y

string; colname for nominal/adj p-values

pCutoff

numeric; value to set p value cutoff

FCcutoff

numeric; value to set log fold change cutoff

xlab_high

string; description of high x values (\u2191 for up arrow!)

xlab_low

string; description of low x values (\u2193 for down arrow!)

xlab_size

numeric; size of x labels

title

string; plot title

subtitle

string; plot subtitle

savename

string; full name of file to save under

height

numeric; saved plot height

width

numeric; saved plot width

Value

ggplot2 volcano plot