bioconductor-geneplotter

name	bioconductor-geneplotter
description	Functions for plotting genomic data
when_to_use	Use when: Visualizing microarray or high-throughput genomic data along chromosomes using cPlot and cColor.; Plotting characteristics of expression levels over contiguous regions of a single chromosome using alongChrom.; Assembling and plotting chromLocation objects to map experimental probe data to physical chromosome locations via buildChromLocation.. Not for: For modern, highly customizable genomic track visualizations (e.g., plotting RNA-seq coverage, BAM alignments, and gene annotations together), use Gviz or ggbio instead.; For general-purpose high-dimensional data visualization (like PCA, t-SNE, or vo
user-invocable	false

geneplotter

Functions for plotting genomic data.

Dependencies & Environment

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

• Version: 1.90.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: Biobase, BiocGenerics, lattice, annotate
• Imports: AnnotationDbi, RColorBrewer
• System requirements: URL
• Install: BiocManager::install("geneplotter")

When to Use

• Visualizing microarray or high-throughput genomic data along chromosomes using cPlot and cColor.
• Plotting characteristics of expression levels over contiguous regions of a single chromosome using alongChrom.
• Assembling and plotting chromLocation objects to map experimental probe data to physical chromosome locations via buildChromLocation.

When NOT to Use

• For modern, highly customizable genomic track visualizations (e.g., plotting RNA-seq coverage, BAM alignments, and gene annotations together), use Gviz or ggbio instead.
• For general-purpose high-dimensional data visualization (like PCA, t-SNE, or volcano plots), use ggplot2 or ComplexHeatmap instead.

Data Requirements

• Input: ExpressionSet objects (e.g., sample.ExpressionSet) or numeric matrices of genomic data.
• Annotation: Requires annotation packages (e.g., hu6800.db, hgu95av2.db) to build chromLocation objects and map probe IDs to chromosomal coordinates.

Key Parameters

• useChroms: A character vector specifying which chromosomes to plot in cPlot.
• plotFormat: Format of the plot in alongChrom (e.g., "cumulative").
• col: Color vector for distinguishing chromosomes or experimental groups in cColor or alongChrom.

Best Practices

• Use buildChromLocation with the appropriate Bioconductor annotation package name (e.g., "hu6800", "hgu95av2") to construct the chromLocation object.
• Reorder chromosomes in the chromLocation object numerically before plotting with cPlot to ensure a logical layout.
• Set up appropriate device dimensions (e.g., using layout or par) when using cPlot to ensure chromosome labels and data points do not overlap.

Common Pitfalls

• Mismatched genome builds: Mapping probe data using an outdated annotation package while comparing to coordinates from a newer genome build. Fix: Double-check the source of the metadata and use matching Bioconductor annotation packages.
• Genes mapped to multiple chromosomes: Some genes (e.g., in pseudoautosomal regions) may map to multiple chromosomes, causing issues. Fix: Filter or assign these genes to a single chromosome before building the location object.

Alternatives

• Gviz: For plotting highly customizable, publication-quality genomic tracks.
• ggbio: For grammar-of-graphics based genomic data visualization.
• RIdeogram: For idiogram-based visualization of genome-wide data across chromosomes.

Citations

• Gentleman R. (2023). "geneplotter: Graphic related functions for Bioconductor." R package version 1.84.0.

References

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

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