biovizBase

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
• Imports: scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors, IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biostrings, Rsamtools, GenomicAlignments, GenomicFeatures, AnnotationDbi, VariantAnnotation, ensembldb, AnnotationFilter, rlang
• System requirements: URL
• Install: BiocManager::install("biovizBase")

When to Use

• Generating colorblind-safe palettes for biological data visualization using colorBlindSafePal().
• Retrieving standardized, biologically sensible color schemes for cytobands, strands, or nucleotides using getBioColor().
• Manipulating GRanges objects for plotting by adding disjoint stepping levels (addStepping()) or shrinking gaps (shrinkageFun()).
• Fetching chromosome ideograms from the UCSC genome browser using getIdeogram().

When NOT to Use

• For high-level, out-of-the-box static genomic plotting, use ggbio because biovizBase only provides the low-level utilities and color schemes.
• For interactive genomic graphics, use visnab because biovizBase is designed as a foundational infrastructure package rather than an interactive plotting tool.

Data Requirements

• Input Format: GRanges objects (from the GenomicRanges package) for genomic manipulations, or character vectors of biological categories (e.g., "A", "C", "T", "G", "N") for color mapping.
• Structure: Genomic coordinates must be properly formatted in GRanges to use utilities like addStepping(), maxGap(), or gaps().

Key Parameters

• repeatable (TRUE): Controls whether to repeat colors if the required number exceeds the maximum colors allowed in colorBlindSafePal().
• source ("default"): Specifies whether to retrieve colors from the default fixed settings or from the user's options in getBioColor().
• extend.size (5): The size to extend ranges when adding stepping levels in addStepping().
• max.gap (0): The maximum gap size allowed when shrinking gaps using shrinkageFun().
• cytoband (TRUE): Logical indicating whether to include cytoband information when fetching an ideogram with getIdeogram().

Best Practices

• Use getBioColor() instead of accessing options directly to hide internal complexity and ensure uniform color schemes across all graphics.
• Check custom color palettes for colorblind safety using dichromat() to ensure accessibility for deuteranopia and protanopia.
• Use plotColorLegend() or showColor() to visually verify your selected color schemes before applying them to complex genomic plots.

Common Pitfalls

• Running out of colors in a palette: Requesting more colors than a specific colorblind-safe palette supports returns NA or errors. Fix: Set repeatable = TRUE when calling the function returned by colorBlindSafePal().
• Inconsistent color themes across plots: Hardcoding colors leads to mismatched figures. Fix: Temporarily edit colors in the global options (options(biovizBase = opts)) so getBioColor() returns uniform colors globally.

Alternatives

• ggbio: Built on top of biovizBase, use this for actual static genomic plotting rather than just base utilities.
• visnab: Built on top of biovizBase, use this for interactive genomic graphics.
• RColorBrewer: Provides general color palettes, but lacks the built-in biological category mappings (like nucleotides or cytobands) provided by biovizBase.
• dichromat: Used for colorblindness simulation, but does not provide genomic-specific color generators out of the box.

Citations

• Tengfei Yin, Michael Lawrence, Dianne Cook (2026). "An Introduction to biovizBase".

References

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

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