| name | bioconductor-enhancedvolcano |
| description | Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many po |
| when_to_use | Use when: Publication-Ready Visualization: Creating highly-configurable volcano plots from differential expression results using the EnhancedVolcano() function.; Targeted Gene Labeling: Visualizing specific genes of interest by supplying a vector of variables to the selectLab parameter.; Highlighting Key Variables: Emphasizing specific points by encircling them or shading them using the encircle and shade p. Not for: For performing differential expression analysis: Use DESeq2 (e.g., DESeq() and results()) instead, because EnhancedVolcano only visualizes the statistical output.; For mapping gene identifiers: Use mapIds() from AnnotationDbi instead, as EnhancedVolc |
| user-invocable | false |
EnhancedVolcano
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.30.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: ggplot2, ggrepel
- Imports: scales
- Install:
BiocManager::install("EnhancedVolcano")
When to Use
- Publication-Ready Visualization: Creating highly-configurable volcano plots from differential expression results using the
EnhancedVolcano() function.
- Targeted Gene Labeling: Visualizing specific genes of interest by supplying a vector of variables to the
selectLab parameter.
- Highlighting Key Variables: Emphasizing specific points by encircling them or shading them using the
encircle and shade parameters.
When NOT to Use
- For performing differential expression analysis: Use
DESeq2 (e.g., DESeq() and results()) instead, because EnhancedVolcano only visualizes the statistical output.
- For mapping gene identifiers: Use
mapIds() from AnnotationDbi instead, as EnhancedVolcano requires the labels to be pre-formatted and mapped before plotting.
Data Requirements
- A data-frame, data-matrix, or tibble of test results containing point labels, log2 fold changes, and adjusted or unadjusted P values.
Key Parameters
- lab: A vector of point labels (e.g.,
rownames(res)).
- x: The column name in the results object containing log2 fold changes (e.g., 'log2FoldChange').
- y: The column name in the results object containing P values (e.g., 'pvalue').
- pCutoff (10e-6): The statistical significance threshold for P values.
- FCcutoff (2.0): The threshold for absolute log2 fold changes.
- drawConnectors: A logical indicating whether to add connectors from labels to points to maximize free space.
- colCustom: A named vector of custom key-value pairs to over-ride the default colour scheme.
- boxedLabels: A logical indicating whether to draw simple boxes around the plot's labels to improve clarity.
Best Practices
- Use
lfcShrink() from DESeq2 to obtain moderated 'shrunk' estimates of log2FC differences before plotting.
- Set
drawConnectors = TRUE to fit more labels in the plot window without overcrowding the points.
- Use
parseLabels = TRUE along with italic() to parse and present labels as italicised text.
- Disable default gridlines (
gridlines.major = FALSE, gridlines.minor = FALSE) to make extra threshold lines (hline, vline) more visible.
Common Pitfalls
- Overcrowded labels: Too many significant genes can clog up the plot. Fix: Use the
selectLab parameter to only label key variables of interest.
- Legend taking up too much space: The default legend might obscure data. Fix: Change
legendPosition to 'none' to make the legend completely invisible.
- Missing dependencies for encircling: Attempting to encircle points without the required dependencies will fail. Fix: Ensure the
ggalt package is installed before using the encircle parameter.
Alternatives
- ggplot2: The underlying engine for EnhancedVolcano, which can be used directly for fully custom plots but requires more manual configuration for label repulsion and cutoffs.
- ggrepel: Provides the label repulsion engine used internally by EnhancedVolcano, useful if building a custom volcano plot from scratch.
Citations
References
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