genomewide.lsn.plot: Genome-wide Lesion Plot
In GRIN2: Genomic Random Interval (GRIN)

genomewide.lsn.plot

R Documentation

Genome-wide Lesion Plot

Description

Generates a genome-wide lesion plot displaying genomic lesions across chromosomes and patients, together with lesion recurrence and statistical significance from the GRIN analysis.

Usage

genomewide.lsn.plot(grin.res,
                    ordered = FALSE,
                    pt.order = NULL,
                    lsn.colors = NULL,
                    max.log10q = NULL)

Arguments

`grin.res`	GRIN results (output from the `grin.stats` function).
`ordered`	Logical; if `TRUE`, patients are displayed according to the order specified in `pt.order`. If `FALSE` (default), patient IDs are ordered alphabetically.
`pt.order`	A data frame with two columns: `"ID"` containing patient identifiers matching those in the lesion data, and `"pts.order"` containing the numeric plotting order from 1 to the total number of patients. Required only when `ordered = TRUE`.
`lsn.colors`	A named vector of colors assigned to lesion types. Names must correspond to lesion types in the GRIN results. If `NULL`, colors are automatically assigned using `default.grin.colors`.
`max.log10q`	Numeric; optional maximum value of -log10(q-value) displayed in the left panel. Values greater than `max.log10q` are capped at this value. If `NULL`, the plotting limit is determined automatically from the observed finite -log10(q-values).

Details

The function first uses compute.gw.coordinates to convert chromosome-specific genomic coordinates into continuous genome-wide coordinates used for plotting lesions across the genome.

The resulting plot contains three aligned panels. The center panel displays genomic lesions across patients and chromosomes. Each patient occupies one column, and lesions are colored according to lesion type. The left panel displays the -log10(q-value) for each gene-lesion type combination from the GRIN analysis, whereas the right panel displays the corresponding number of affected patients.

By default, patients are ordered alphabetically by patient ID. A user-defined patient order can instead be supplied through pt.order by setting ordered = TRUE.

Value

Generates a genome-wide lesion plot on the active graphics device and invisibly returns NULL. The plot consists of three aligned panels:

Left panel: Displays the statistical significance of lesion recurrence for each gene and lesion type as -log10(q-value). Horizontal lines are colored by lesion type, with longer lines representing greater statistical significance.
Middle panel: Displays the genome-wide distribution of lesions across chromosomes and patients. Each column represents a patient, chromosomes are arranged consecutively along the vertical axis, and lesions are colored according to lesion type.
Right panel: Displays the number of patients affected by each lesion type at each gene. Horizontal lines are colored by lesion type, with longer lines representing a greater number of affected patients.

Author(s)

Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org

References

Pounds, S., et al. (2013). A genomic random interval model for statistical analysis of genomic lesion data.

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

Examples

data(lesion_data)
data(hg38_gene_annotation)
data(hg38_chrom_size)

# Run GRIN analysis
grin.results <- grin.stats(lesion_data,
                           hg38_gene_annotation,
                           hg38_chrom_size)

# Generate genome-wide lesion plot with alphabetical patient ordering
genomewide.lsn.plot(grin.results,
                    max.log10q = 50)


# Generate plot using a user-defined patient order, such as grouping patients
patient.ids <- sort(unique(lesion_data$ID))
pt.order <- data.frame(ID = patient.ids,
                       pts.order = seq_along(patient.ids))

genomewide.lsn.plot(grin.results,
                    ordered = TRUE,
                    pt.order = pt.order,
                    max.log10q = 50)

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