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bioconductor-gviz

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to

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bioconductor-gviz

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Use bioconductor-gviz to provide R code for a genome-browser-style plot of [genomic features or coverage data] across [genome build, chromosome, and coordinate range], with suitable tracks and display settings.

Required inputs

  • [genomic features or coverage data]
  • [genome build, chromosome, and coordinate range]

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SKILL.md

name: bioconductor-gvizdescription: Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this towhen_to_use: "Use when: 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 UC. Not for: 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"user-invocable: false

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

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