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generate_complex_oncoprint

generate_complex_oncoprint is an R function that utilizes the jokergoo/ComplexHeatmap package to create oncoprints for visualizing variants, including mutations (required), copy number variants (CNVs) (optional), and structural variants (SVs) (optional). The function provides publication-ready visuals with easily adjustable aesthetics.

The colors follow mutation effects based on the Isabl pipeline default formats (Elli Papaemanuil’s Lab).

🚀 Installation

To install ComplexHeatmap, ensure you have Bioconductor installed:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")

📌 Usage

Simple Example

source("./generate_complex_oncoprint.R")

ht <- generate_complex_oncoprint(
    muts = MUT, 
    show.sample.names = TRUE, 
    show.border = FALSE,
    min.freq = 1, 
    show.title = TRUE, 
    title.str = "Example 1 - YOHOOOO oncoprint with NO ERROR!", 
    save.name = "Example_1.A",
    save.path = "./example_oncoprints/"
)

📊 Features

  • Supports:
    • Mutations (required)
    • Copy Number Variants (CNVs, optional)
    • Structural Variants (SVs, optional)
  • Customizable aesthetics for publication-quality figures.
  • Annotation banners: Add categorical variables from a lookup table as bottom annotations: 
    show.another.banner = TRUE
banner.name = c("FEATURE.COL.1", "FEATURE.COL.2", ...)
  • Paired sample oncoprint for pre/post visualization (experimental, may throw errors).
  • Timepoint visualization: Option to show a heatbar for samples from the same patient.
  • Annotation barplots: Examples available in BOTTOM_annot script for specific projects (not yet integrated into parameter-based runs).

📁 File Structure

  • Example script & documentation: Refer to example files for more details on function usage.
  • Recognized terms for mutation, CNV, and SV types (column: EFFECT):
    • Refer to: ~/Complex_Oncoprint/sub_function/test_required_fields.R.

⚠️ Notes

  • Paired sample oncoprint is available but may need updates.
  • If you need a specific mutation representation, please reach out.

📩 Contact: [email protected]

🙌 Acknowledgments

Thanks to Zuguang Gu for the ComplexHeatmap package!
🔗 https://github.com/jokergoo/ComplexHeatmap

Last updated: February 2025