grin.stats.lsn.plot: GRIN Lesion and Statistics Plot

In GRIN2: Genomic Random Interval (GRIN)

GRIN Lesion and Statistics Plot

Description

Generates a regional plot showing genomic lesions overlapping a selected feature together with its GRIN statistics. This function is particularly designed for regulatory and other genomic features that do not have transcript or exon structure to display.

Usage

grin.stats.lsn.plot(grin.res,
                    feature = NULL,
                    lsn.clrs = NULL,
                    expand = 0.0005)

Arguments

grin.res	GRIN results for genes, regulatory elements, or other genomic features, as returned by the grin.stats function.
feature	Character string specifying the feature of interest. This is typically an Ensembl regulatory feature ID or another regulatory-region identifier used as marker input to grin.stats. An Ensembl gene ID can also be provided.
lsn.clrs	A named vector of colors assigned to lesion types. If NULL, colors are automatically assigned using default.grin.colors.
expand	Numeric; proportion of the feature length added upstream and downstream to define the plotting region. Default is 0.0005. Setting expand = 0 restricts the plot to the exact feature boundaries.

Details

This function provides a regional visualization of lesions and GRIN statistics without displaying transcript or exon structure. It is therefore particularly useful for regulatory features, such as promoters, enhancers, CTCF binding sites, open chromatin regions, or other genomic elements for which a transcript panel is not applicable.

Genes can also be plotted with this function when only the lesion distribution and GRIN statistics are needed. However, for gene-centered visualization that includes transcript and exon structure, lsn.transcripts.plot is generally more informative.

The plot contains a regional lesion panel followed by statistical summaries:

• The upper panel displays individual genomic lesions overlapping the selected feature. Each row represents one overlapping lesion event, and lesions are colored according to lesion type. Dashed vertical lines mark the start and end coordinates of the selected feature.

• The first statistical summary reports, for each lesion type, the number of affected subjects together with the corresponding -\log_{10}(p) and -\log_{10}(q) values from the GRIN lesion-recurrence analysis.

• The second statistical summary reports the constellation -\log_{10}(p) and -\log_{10}(q) values across lesion orders evaluated by GRIN.

Value

Generates a regional lesion and GRIN statistics plot on the active graphics device and invisibly returns NULL. No transcript or exon annotation panel is included.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

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

See Also

grin.stats, lsn.transcripts.plot, default.grin.colors

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)

# Plot lesions and GRIN statistics for a gene without displaying
# transcript or exon structure
grin.stats.lsn.plot(grin.results,
                    feature = "ENSG00000184937")

# This function is particularly useful when regulatory elements or other
# non-transcript genomic features are used as marker input to grin.stats.
# For gene-centered plots that include transcript and exon annotation,
# use lsn.transcripts.plot().

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