volcanoPlot: Volcano plots

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

Volcano plots

Description

Volcano plot for each comparison: -log10(adjusted P value) vs log2(FC) with one dot per feature (red dot for a differentially expressed feature, black dot otherwise)

Usage

volcanoPlot(
  complete,
  alpha = 0.05,
  outfile = TRUE,
  padjlim = NULL,
  ggplot_theme = theme_gray()
)

Arguments

complete	A list of data.frame containing features results (from exportResults.DESeq2() or exportResults.edgeR())
alpha	cut-off to apply on each adjusted p-value
outfile	TRUE to export the figure in a png file
padjlim	numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)
ggplot_theme	ggplot2 theme function (theme_gray() by default)

Value

A file named volcanoPlot.png in the figures directory containing one volcano plot per comparison

Author(s)

Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.