# Bioconductor Geneplotter

> Functions for plotting genomic data

- Skill: `biomate-ai/bioconductor-geneplotter` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biomate-ai/bioconductor-geneplotter`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biomate-ai/bioconductor-geneplotter/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: biomate-ai (https://skillmd.com/u/biomate-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biomate-ai/bioconductor-geneplotter

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# 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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## Run this on BioMate

This skill is the **knowledge layer** — when, why, and how to use `geneplotter`. To **run this analysis on your own data** with managed compute, automated QC, and reproducible outputs, use **[BioMate](https://www.biomate.ai?ref=kb&pkg=geneplotter)** — free to start.

▶ **[Open `geneplotter` on BioMate →](https://www.biomate.ai?ref=kb&pkg=geneplotter)**