genomewide.log10q.plot: Genome-wide -log10(q-value) Plot
In GRIN2: Genomic Random Interval (GRIN)

genomewide.log10q.plot

R Documentation

Genome-wide -log10(q-value) Plot

Description

Generates a genome-wide plot of -log10(q-values) for each annotated gene or lesion boundary evaluated by GRIN. Statistical significance can be displayed for one or more selected lesion types.

Usage

genomewide.log10q.plot(grin.res,
                       lsn.grps,
                       lsn.colors = NULL,
                       max.log10q = NULL)

Arguments

`grin.res`	GRIN results object (output from `grin.stats`) generated using either gene annotation or lesion boundaries as marker input.
`lsn.grps`	A character vector specifying the lesion type(s) to include in the plot.
`lsn.colors`	A named vector of colors corresponding to the selected lesion types. If `NULL`, colors are automatically assigned using `default.grin.colors`.
`max.log10q`	Numeric; optional maximum value of -log10(q-value) displayed on the plot. 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

This function displays the genome-wide statistical significance of lesions affecting annotated genomic markers. Depending on the marker data supplied to grin.stats, these markers may represent genes or lesion boundaries.

The function first adds continuous genome-wide plotting coordinates using compute.gw.coordinates when these coordinates are not already present in grin.res.

Chromosomes are arranged consecutively along the vertical axis. For each selected lesion type, a horizontal line is drawn at the genomic position of each affected marker. Line length represents the corresponding -log10(q-value), with longer lines indicating greater statistical significance, and line color identifies the lesion type.

Value

Generates a genome-wide -log10(q-value) plot on the active graphics device and invisibly returns NULL. Chromosomes are displayed along the vertical axis, while the horizontal axis represents -log10(q-value). Each horizontal line corresponds to an affected gene or lesion boundary, with line length representing statistical significance and line color indicating lesion type.

Author(s)

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

References

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)

# Use lesion boundaries as genomic markers for gain lesions
gain <- lesion_data[lesion_data$lsn.type == "gain", ]
lsn.bound.gain <- grin.lsn.boundaries(gain,
                                      hg38_chrom_size)

GRIN.results.gain.bound <- grin.stats(gain,
                                      lsn.bound.gain,
                                      hg38_chrom_size)

# Plot genome-wide significance of gain lesion boundaries
genomewide.log10q.plot(GRIN.results.gain.bound,
                       lsn.grps = "gain",
                       lsn.colors = c("gain" = "red"),
                       max.log10q = 10)

# Gene annotation can also be used as the marker input to grin.stats instead
# of lesion boundaries.
# Multiple lesion types can be displayed together by including their names
# in lsn.grps.

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