onco.print.props: Oncoprint Proportions by Lesion Type

In GRIN2: Genomic Random Interval (GRIN)

Oncoprint Proportions by Lesion Type

Description

Calculates and assigns the proportion of each oncoprint rectangle to be color-filled based on the average size of lesion types. Lesion types are ordered by their average genomic size, and proportions are either computed automatically or manually specified by the user.

Usage

onco.print.props(lsn.data, clr = NULL, hgt = NULL)

Arguments

lsn.data	A data frame with five columns: ID: Subject or patient identifier chrom: Chromosome on which the lesion is located loc.start: Start genomic position of the lesion loc.end: End genomic position of the lesion lsn.type: Lesion category (e.g., gain, mutation, fusion) Lesion type names in lsn.type must be valid R variable names (e.g., mutation, fusion, or gain) and must not contain spaces or other special characters.
clr	Optional. A named vector of colors for each lesion type. User-specified colors are preserved and matched to lesion types by name. If not provided, default colors are assigned using default.grin.colors.
hgt	Optional. A named numeric vector specifying the proportion (height) of the oncoprint rectangle to be filled for each lesion type. If not provided, proportions are determined automatically based on average lesion sizes.

Details

In cases where a patient has multiple types of lesions (e.g., gain and mutation) in the same gene, this function ensures that all lesion types are visually represented within a single oncoprint rectangle.

If hgt is not specified, lesion types are ranked by their average genomic size (calculated as loc.end - loc.start + 1), and the oncoprint proportions are derived accordingly. Smaller lesions (such as point mutations) occupy a smaller portion of the rectangle, while larger lesions (such as copy-number alterations) occupy a larger portion.

Alternatively, the user can manually define the fill proportions using the hgt parameter.

Colors can be manually specified using a named vector supplied to clr. When custom colors are provided, they are matched to lesion types by name and retained in the resulting oncoprint settings.

Value

A list with the following components:

• alter_func: A list of alteration-drawing functions for rendering the different lesion types in the oncoprint.

• col: A named vector of colors assigned to each lesion type.

• heatmap_legend_param: Legend parameters for the oncoprint.

Author(s)

Lakshmi Patibandla [e-mail], Abdelrahman Elsayed [e-mail], Stanley Pounds [e-mail]

References

Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.

Examples

data(lesion_data)

# Automatically assign oncoprint proportions based on average lesion size:
onco.props <- onco.print.props(lesion_data)

# Manually specify the oncoprint fill proportions for each lesion type:
onco.props <- onco.print.props(
  lesion_data,
  hgt = c(
    "gain" = 4,
    "loss" = 3,
    "mutation" = 2,
    "fusion" = 1
  )
)

# Specify custom colors for lesion types:
custom.colors <- c(
  "gain" = "red",
  "loss" = "blue",
  "mutation" = "olivedrab",
  "fusion" = "black"
)

onco.props <- onco.print.props(
  lesion_data,
  clr = custom.colors
)

GRIN2 documentation built on Aug. 22, 2026, 5:09 p.m.