Bioconductor Enhancedvolcano

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

• Blighe, K, S Rana, and M Lewis. 2018. “EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling.” https://github.com/kevinblighe/EnhancedVolcano.

References

• Homepage: https://bioconductor.org/packages/EnhancedVolcano
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.pdf

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