ggbio

Dependencies & Environment

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

• Version: 1.60.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: BiocGenerics, ggplot2
• Imports: gridExtra, scales, reshape2, gtable, Hmisc, biovizBase, Biobase, S4Vectors, IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biostrings, Rsamtools, GenomicAlignments, BSgenome, VariantAnnotation, rtracklayer, GenomicFeatures, OrganismDbi, ensembldb, AnnotationDbi, AnnotationFilter, rlang
• Install: BiocManager::install("ggbio")

When to Use

• Construct an ideogram track for a specific genome (e.g., hg19) using Ideogram.
• Plot gene models from OrganismDb, TxDb, or EnsDb objects using autoplot.
• Visualize zoomed regions on an ideogram by passing a GRanges object to xlim.

When NOT to Use

• For fetching specific gene/transcript information with a rich filtering system (use ensembldb instead).
• For purely retrieving gene annotations without visualization (use Homo.sapiens or TxDb directly).

Data Requirements

• Input data should be Bioconductor objects like OrganismDb, TxDb, EnsDb, GRanges, or GRangesList.
• Ideograms require specifying a supported genome build (e.g., "hg19", "mm10").

Key Parameters

• genome (default): Specifies the genome build (e.g., "hg19") for the Ideogram function.
• which (default): A GRanges object used to subset the region of interest in autoplot.
• gap.geom (default): Controls the geometry of introns (e.g., "chevron") in gene model tracks.
• stat (default): Statistical transformation, such as "reduce" to collapse all features.
• columns (default): Specifies which columns to retrieve for labeling from an OrganismDb object.
• names.expr (default): An expression to create flexible label combinations from column names.
• label.color (default): Controls the text color of the labels in autoplot.
• fill (default): Controls the fill color of the plotted features.

Best Practices

• Use OrganismDb or EnsDb objects over TxDb if you need to label transcripts with gene symbols.
• Use stat = "reduce" in autoplot to collapse all features and simplify the gene model track.
• Use names.expr to combine multiple metadata columns (like TXNAME and GO) into a single track label.

Common Pitfalls

• Attempting to label a TxDb gene model track with gene symbols. Fix: TxDb doesn't contain gene symbols; use an OrganismDb or EnsDb object instead.
• Ideogram zoom highlights not appearing correctly. Fix: Use xlim with a GRanges object to change the highlighted zoomed region on the ideogram.
• Overlapping or cluttered gene models in dense regions. Fix: Use stat = "reduce" to collapse features or filter the input object before plotting.

Alternatives

• ensembldb: For filtering and fetching Ensembl annotations rather than plotting them.
• ggplot2: For general-purpose grammar of graphics plotting without specialized genomic geoms.
• biovizBase: For underlying genomic data transformations that feed into visualizations.

Citations

• Yin, T., Cook, D., & Lawrence, M. (2012). ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology, 13(8), R77.

References

• Homepage: bioconductor.org/packages/ggbio
• Vignette: vignette_0_23da92f0.txt

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