plot_volcano: Volcano Plot

In dswatson/bioplotr: Pretty, simple, optionally interactive plots for bioinformatics analysis pipelines

Volcano Plot

Description

This function plots effect size against significance for a given test of differential expression.

Usage

plot_volcano(
  dat,
  y = "p",
  fdr = 0.05,
  lfc = NULL,
  probes = NULL,
  size = NULL,
  alpha = NULL,
  title = "Volcano Plot",
  legend = "right",
  hover = FALSE
)

Arguments

dat	Data frame or similar object representing the results of a test for differential expression, such as the output of a call to limma::topTable, edgeR::topTags, or DESeq2::results. Alternatively, any object coercable to a data frame with columns for p-values, q-values, and log fold changes. Missing values are silently removed.
y	Plot p-values (y = "p"), q-values (y = "q"), or log-odds (y = "B") on the y-axis?
fdr	Significance threshold for declaring a probe differentially expressed.
lfc	Optional effect size threshold for declaring a probe differentially expressed.
probes	Optional column number or name specifying where probe names are stored, presuming they are not stored in rownames(dat).
size	Point size.
alpha	Point transparency.
title	Optional plot title.
legend	Legend position. Must be one of "bottom", "left", "top", "right", "bottomright", "bottomleft", "topleft", or "topright".
hover	Show probe name by hovering mouse over data point? If TRUE, the plot is rendered in HTML and will either open in your browser's graphic display or appear in the RStudio viewer. Probe names are extracted from dat.

Details

Volcano plots visualize the relationship between each probe's effect size and significance for a given test of differential expression. Points are colored to distinguish between those that do and do not meet a user-defined FDR threshold. Up- and down-regulated genes may also be differentially colored if a minimum absolute fold change is supplied. These figures help to evaluate the symmetry, magnitude, and significance of effects in an omic experiment.

Examples

# Simulated data
library(DESeq2)
dds <- makeExampleDESeqDataSet()
dds <- DESeq(dds)
res <- results(dds)
plot_volcano(res)

# Real data
data(airway)
dds <- DESeqDataSet(airway, design = ~ cell + dex)
dds <- DESeq(dds)
res <- results(dds)
plot_volcano(res)

dswatson/bioplotr documentation built on March 3, 2023, 9:43 p.m.