| name | bioconductor-biovizbase |
| description | The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and enc |
| when_to_use | Use when: 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. Not for: 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 infrastructur |
| user-invocable | false |
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
Run this on BioMate
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