Gviz

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.56.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: S4Vectors, IRanges, GenomicRanges
• Imports: XVector, rtracklayer, lattice, RColorBrewer, biomaRt, AnnotationDbi, Biobase, GenomicFeatures, ensembldb, BSgenome, Biostrings, biovizBase, Rsamtools, latticeExtra, matrixStats, GenomicAlignments, Seqinfo, GenomeInfoDb, BiocGenerics, digest
• Install: BiocManager::install("Gviz")

When to Use

• Plotting genomic data and annotation features (e.g., CpG islands, gene models) in a genome browser-like layout using plotTracks.
• Visualizing run-length encoded numeric vectors or matrices (like NGS read coverage or microarray probes) using DataTrack.
• Adding a genomic axis with coordinate tick-marks and directional indicators using GenomeAxisTrack.
• Displaying chromosome ideograms fetched from UCSC using IdeogramTrack.

When NOT to Use

• For purely statistical analysis of genomic data without visualization, use dedicated analysis packages instead because Gviz is strictly a visualization framework.
• For interactive, web-based genome browsing, use tools like IGV or UCSC Genome Browser instead because Gviz generates static plots via the grid graphics system.

Data Requirements

• Genomic features: Represented as GRanges, IRanges, or data.frame objects.
• Identifiers: Valid UCSC genome and chromosome identifiers (e.g., chr7 on mm9) for fetching online annotation data.
• Sequence information: A BSgenome package (e.g., BSgenome.Hsapiens.UCSC.hg19) for SequenceTrack.

Key Parameters

• from / to: Arbitrary genomic range coordinates to restrict the plotted region in plotTracks.
• extend.left / extend.right: Relative zoom factors or absolute integer values to extend the currently displayed range.
• type: The plotting type for numeric data in DataTrack (e.g., "histogram", "dot").
• reverseStrand: Logical parameter to plot data relative to the opposite (3' -> 5') strand.
• showId: Logical scalar to show optional range highlighting annotation in GenomeAxisTrack.
• labelPos: Controls the arrangement of tick marks (e.g., "alternating", "above", "below").

Best Practices

• Use availableDisplayPars to discover which display parameters control the appearance of a specific track class.
• Register custom display parameter modifications globally using addScheme and options(Gviz.scheme = "myScheme") to avoid repetitive typing.
• Ensure chromosome names follow the UCSC definition (starting with "chr") when fetching data from online repositories, or disable the check via options(ucscChromosomeNames=FALSE).

Common Pitfalls

• Slow plotting or timeouts: Occurs when fetching large ideogram or annotation data from UCSC; fix this by caching data locally or plotting smaller genomic regions.
• Overplotting of features: Occurs when features are too close together for the current device resolution; fix this by zooming in using the from and to arguments in plotTracks.
• Mixture of forward and reverse strand tracks: Occurs when combining tracks with different strand orientations; fix this by setting reverseStrand = TRUE globally in plotTracks rather than per track.

Alternatives

• GenomeGraphs: An older package that Gviz is loosely based on, but Gviz offers increased performance and flexibility.
• rtracklayer: Used for importing/exporting genomic annotations and connecting to browsers, but lacks the native R grid graphics plotting capabilities of Gviz.

Citations

• Hahne F and Ivanek R (2016). Visualizing Genomic Data Using Gviz and Bioconductor. Methods in molecular biology (Clifton, N.J.), 1418, 335-51.

References

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

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