GRIN2 (version 2.0.0)

genomewide.log10q.plot: 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. The plot is lesion-type specific (e.g., gain, loss, mutation).

Usage

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

Value

A genome-wide plot showing -log10(q-values) for genes or lesion boundaries associated with specific lesion types.

Arguments

grin.res

GRIN results object (output from grin.stats) using either gene annotation or lesion boundaries as marker input.

lsn.grps

A character vector specifying which lesion group(s) to include in the plot.

lsn.colors

A named vector of colors corresponding to each lesion group. If NULL, default colors will be assigned using the default.grin.colors() function.

max.log10q

Numeric; maximum value for -log10(q-value) displayed on the plot. Any value above this threshold will be capped at max.log10q.

Author

Abdelrahman Elsayed and Stanley Pounds

Details

This function visualizes the significance of lesions affecting genomic loci across chromosomes. It plots -log10(q-values) for either gene-based or lesion-boundary markers based on the GRIN analysis. The plot is faceted or colored by lesion group (e.g., gain, loss).

See Also

grin.lsn.boundaries

Examples

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

# Example 1: Use lesion boundaries for gains
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)

genomewide.log10q.plot(GRIN.results.gain.bound,
                       lsn.grps = c("gain"),
                       lsn.colors = c("gain" = "red"),
                       max.log10q = 10)

# hg38_gene_annotation can be used instead of the boundaries as the marker data.

# This function can be used similarly for other lesion types (e.g., loss, mutation).